Methods and compositions for cellular and metabolic engineering

ABSTRACT

The present invention is generally directed to the evolution of new metabolic pathways and the enhancement of bioprocessing through a process herein termed recursive sequence recombination. Recursive sequence recombination entails performing iterative cycles of recombination and screening or selection to &#34;evolve&#34; individual genes, whole plasmids or viruses, multigene clusters, or even whole genomes. Such techniques do not require the extensive analysis and computation required by conventional methods for metabolic engineering.

This application is a continuation of U.S. patent application Ser. No.08/650,400 filed May 20, 1996, now U.S. Pat. No. 5,837,458, which is acontinuation-in-part of U.S. patent application Ser. No. 08/621,430filed Mar. 25, 1996 (abandoned) and of Ser. No. 08/621,859 filed Mar.25, 1996, now U.S. Pat. No. 6,117,679, and of Ser. No. 08/537,874 filedMar. 4, 1996 which is the U.S. National Phase of PCT/US95/02126 filedFeb. 17, 1995 and is now U.S. Pat. No. 5,830,721 and of Ser. No.08/198,431 filed Feb. 17, 1994, now U.S. Pat. No. 5,605,793, thespecifications of which are incorporated herein by reference in theirentirety for all purposes.

COPYRIGHT NOTIFICATION

Pursuant to 37 C.F.R. 1.71(e), Applicants note that a portion of thisdisclosure contains material which is subject to copyright protection.The copyright owner has no objection to the facsimile reproduction byanyone of the patent document or patent disclosure, as it appears in thePatent and Trademark Office patent file or records, but otherwisereserves all copyright rights whatsoever.

BACKGROUND OF THE INVENTION

Metabolic engineering is the manipulation of intermediary metabolismthrough the use of both classical genetics and genetic engineeringtechniques. Cellular engineering is generally a more inclusive termreferring to the modification of cellular properties. Cameron et al.(Applied Biochem. Biotech. 38:105-140 (1993)) provide a summary ofequivalent terms to describe this type of engineering, including“metabolic engineering”, which is most often used in the context ofindustrial microbiology and bioprocess engineering, “in vitro evolution”or “directed evolution”, most often used in the context of environmentalmicrobiology, “molecular breeding”, most often used by Japaneseresearchers, “cellular engineering”, which is used to describemodifications of bacteria, animal, and plant cells, “rational straindevelopment”, and “metabolic pathway evolution”. In this application,the terms “metabolic engineering” and “cellular engineering” are usedpreferentially for clarity; the term “evolved” genes is used asdiscussed below.

Metabolic engineering can be divided into two basic categories:modification of genes endogenous to the host organism to altermetabolite flux and introduction of foreign genes into an organism. Suchintroduction can create new metabolic pathways leading to modified cellproperties including but not limited to synthesis of known compounds notnormally made by the host cell, production of novel compounds (e.g.polymers, antibiotics, etc.) and the ability to utilize new nutrientsources. Specific applications of metabolic engineering can include theproduction of specialty and novel chemicals, including antibiotics,extension of the range of substrates used for growth and productformation, the production of new catabolic activities in an organism fortoxic chemical degradation, and modification of cell properties such asresistance to salt and other environmental factors.

Bailey (Science 252:1668-1675 (1991)) describes the application ofmetabolic engineering to the recruitment of heterologous genes for theimprovement of a strain, with the caveat that such introduction canresult in new compounds that may subsequently undergo further reactions,or that expression of a heterologous protein can result in proteolysis,improper folding, improper modification, or unsuitable intracellularlocation of the protein, or lack of access to required substrates.Bailey recommends careful configuration of a desired genetic change withminimal perturbation of the host.

Liao (Curr. Opin. Biotech. 4:211-216 (1993)) reviews mathematicalmodelling and analysis of metabolic pathways, pointing out that in manycases the kinetic parameters of enzymes are unavailable or inaccurate.

Stephanopoulos et al. (Trends. Biotechnol. 11:392-396 (1993)) describeattempts to improve productivity of cellular systems or effect radicalalteration of the flux through primary metabolic pathways as havingdifficulty in that control architectures at key branch points haveevolved to resist flux changes. They conclude that identification andcharacterization of these metabolic nodes is a prerequisite to rationalmetabolic engineering. Similarly, Stephanopoulos (Curr. Opin. Biotech.5:196-200 (1994)) concludes that rather than modifying the “ratelimiting step” in metabolic engineering, it is necessary tosystematically elucidate the control architecture of bioreactionnetworks.

The present invention is generally directed to the evolution of newmetabolic pathways and the enhancement of bioprocessing through aprocess herein termed recursive sequence recombination. Recursivesequence recombination entails performing iterative cycles ofrecombination and screening or selection to “evolve” individual genes,whole plasmids or viruses, multigene clusters, or even whole genomes(Stemmer, Bio/Technology 13:549-553 (1995)). Such techniques do notrequire the extensive analysis and computation required by conventionalmethods for metabolic engineering. Recursive sequence recombinationallows the recombination of large numbers of mutations in a minimumnumber of selection cycles, in contrast to traditional, pairwiserecombination events.

Thus, because metabolic and cellular engineering can pose the particularproblem of the interaction of many gene products and regulatorymechanisms, recursive sequence recombination (RSR) techniques provideparticular advantages in that they provide recombination betweenmutations in any or all of these, thereby providing a very fast way ofexploring the manner in which different combinations of mutations canaffect a desired result, whether that result is increased yield of ametabolite, altered catalytic activity or substrate specificity of anenzyme or an entire metabolic pathway, or altered response of a cell toits environment.

SUMMARY OF THE INVENTION

One aspect of the invention is a method of evolving a biocatalyticactivity of a cell, comprising:

(a) recombining at least a first and second DNA segment from at leastone gene conferring ability to catalyze a reaction of interest, thesegments differing from each other in at least two nucleotides, toproduce a library of recombinant genes;

(b) screening at least one recombinant gene from the library thatconfers enhanced ability to catalyze the reaction of interest by thecell relative to a wildtype form of the gene;

(c) recombining at least a segment from at least one recombinant genewith a further DNA segment from at least one gene, the same or differentfrom the first and second segments, to produce a further library ofrecombinant genes;

(d) screening at least one further recombinant gene from the furtherlibrary of recombinant genes that confers enhanced ability to catalyzethe reaction of interest in the cell relative to a previous recombinantgene;

(e) repeating (c) and (d), as necessary, until the further recombinantgene confers a desired level of enhanced ability to catalyze thereaction of interest by the cell.

Another aspect of the invention is a method of evolving a gene to conferability to catalyze a reaction of interest, the method comprising:

(1) recombining at least first and second DNA segments from at least onegene conferring ability to catalyze a reaction of interest, the segmentsdiffering from each other in at least two nucleotides, to produce alibrary of recombinant genes;

(2) screening at least one recombinant gene from the library thatconfers enhanced ability to catalyze a reaction of interest relative toa wildtype form of the gene;

(3) recombining at least a segment from the at least one recombinantgene with a further DNA segment from the at least one gene, the same ordifferent from the first and second segments, to produce a furtherlibrary of recombinant genes;

(4) screening at least one further recombinant gene from the furtherlibrary of recombinant genes that confers enhanced ability to catalyze areaction of interest relative to a previous recombinant gene;

(5) repeating (3) and (4), as necessary, until the further recombinantgene confers a desired level of enhanced ability to catalyze a reactionof interest.

A further aspect of the invention is a method of generating a newbiocatalytic activity in a cell, comprising:

(1) recombining at least first and second DNA segments from at least onegene conferring ability to catalyze a first reaction related to a secondreaction of interest, the segments differing from each other in at leasttwo nucleotides, to produce a library of recombinant genes;

(2) screening at least one recombinant gene from the library thatconfers a new ability to catalyze the second reaction of interest;

(3) recombining at least a segment from at least one recombinant genewith a further DNA segment from the at least one gene, the same ordifferent from the first and second segments, to produce a furtherlibrary of recombinant genes;

(4) screening at least one further recombinant gene from the furtherlibrary of recombinant genes that confers enhanced ability to catalyzethe second reaction of interest in the cell relative to a previousrecombinant gene;

(5) repeating (3) and (4), as necessary, until the further recombinantgene confers a desired level of enhanced ability to catalyze the secondreaction of interest in the cell.

Another aspect of the invention is a modified form of a cell, whereinthe modification comprises a metabolic pathway evolved by recursivesequence recombination.

A further aspect of the invention is a method of optimizing expressionof a gene product, the method comprising:

(1) recombining at least first and second DNA segments from at least onegene conferring ability to produce the gene product, the segmentsdiffering from each other in at least two nucleotides, to produce alibrary of recombinant genes;

(2) screening at least one recombinant gene from the library thatconfers optimized expression of the gene product relative to a wildtypeform of the gene;

(3) recombining at least a segment from the at least one recombinantgene with a further DNA segment from the at least one gene, the same ordifferent from the first and second segments, to produce a furtherlibrary of recombinant genes;

(4) screening at least one further recombinant gene from the furtherlibrary of recombinant genes that confers optimized ability to producethe gene product relative to a previous recombinant gene;

(5) repeating (3) and (4), as necessary, until the further recombinantgene confers a desired level of optimized ability to express the geneproduct.

A further aspect of the invention is a method of evolving a biosensorfor a compound A of interest, the method comprising:

(1) recombining at least first and second DNA segments from at least onegene conferring ability to detect a related compound B, the segmentsdiffering from each other in at least two nucleotides, to produce alibrary of recombinant genes;

(2) screening at least one recombinant gene from the library thatconfers optimized ability to detect compound A relative to a wildtypeform of the gene;

(3) recombining at least a segment from the at least one recombinantgene with a further DNA segment from the at least one gene, the same ordifferent from the first and second segments, to produce a furtherlibrary of recombinant genes;

(4) screening at least one further recombinant gene from the furtherlibrary of recombinant genes that confers optimized ability to detectcompound A relative to a previous recombinant gene;

(5) repeating (3) and (4), as necessary, until the further recombinantgene confers a desired level of optimized ability to detect compound A.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a drawing depicting a scheme for in vitro recursive sequencerecombination.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

The invention provides a number of strategies for evolving metabolic andbioprocessing pathways through the technique of recursive sequencerecombination. One strategy entails evolving genes that confer theability to use a particular substrate of interest as a nutrient sourcein one species to confer either more efficient use of that substrate inthat species, or comparable or more efficient use of that substrate in asecond species. Another strategy entails evolving genes that confer theability to detoxify a compound of interest in one or more species oforganisms. Another strategy entails evolving new metabolic pathways byevolving an enzyme or metabolic pathway for biosynthesis or degradationof a compound A related to a compound B for the ability to biosynthesizeor degrade compound B, either in the host of origin or a new host. Afurther strategy entails evolving a gene or metabolic pathway for moreefficient or optimized expression of a particular metabolite or geneproduct. A further strategy entails evolving a host/vector system forexpression of a desired heterologous product. These strategies mayinvolve using all the genes in a multi-step pathway, one or severalgenes, genes from different organisms, or one or more fragments of agene.

The strategies generally entail evolution of gene(s) or segment(s)thereof to allow retention of function in a heterologous cell orimprovement of function in a homologous or heterologous cell. Evolutionis effected generally by a process termed recursive sequencerecombination. Recursive sequence recombination can be achieved in manydifferent formats and permutations of formats, as described in furtherdetail below. These formats share some common principles. Recursivesequence recombination entails successive cycles of recombination togenerate molecular diversity, i.e., the creation of a family of nucleicacid molecules showing substantial sequence identity to each other butdiffering in the presence of mutations. Each recombination cycle isfollowed by at least one cycle of screening or selection for moleculeshaving a desired characteristic. The molecule(s) selected in one roundform the starting materials for generating diversity in the next round.In any given cycle, recombination can occur in vivo or in vitro.Furthermore, diversity resulting from recombination can be augmented inany cycle by applying prior methods of mutagenesis (e.g., error-pronePCR or cassette mutagenesis, passage through bacterial mutator strains,treatment with chemical mutagens) to either the substrates for orproducts of recombination.

I. Formats for Recursive Sequence Recombination

Some formats and examples for recursive sequence recombination,sometimes referred to as DNA shuffling or molecular breeding, have beendescribed by the present inventors and co-workers in co-pendingapplications, U.S. patent application Ser. No. 08/621,430, filed Mar.25, 1996; Ser. No. PCT/US95/02126, filed Feb. 17, 1995; Ser. No.08/621,859, filed Mar. 25, 1996; Ser. No. 08/198,431, filed Feb. 17,1994; Stemmer, Science 270:1510 (1995); Stemmer et al., Gene 164:49-53(1995); Stemmer, Bio/Technology 13:549-553 (1995); Stemmer, Proc. Natl.Acad. Sci. U.S.A. 91:10747-10751 (1994); Stemmer, Nature 370:389-391(1994); Crameri et al. Nature Medicine 2(1):100-102 (1996); Crameri etal. Nature Biotechnology 14:315-319 (1996), each of which isincorporated by reference in its entirety for all purposes.

(1) In Vitro Formats

One format for recursive sequence recombination in vitro is illustratedin FIG. 1. The initial substrates for recombination are a pool ofrelated sequences. The X's in FIG. 1, panel A, show where the sequencesdiverge. The sequences can be DNA or RNA and can be of various lengthsdepending on the size of the gene or DNA fragment to be recombined orreassembled. Preferably the sequences are from 50 bp to 100 kb.

The pool of related substrates can be fragmented, usually at random,into fragments of from about 5 bp to 5 kb or more, as shown in FIG. 1,panel B. Preferably the size of the random fragments is from about 10 bpto 1000 bp, more preferably the size of the DNA fragments is from about20 bp to 500 bp. The substrates can be digested by a number of differentmethods, such as DNAseI or RNAse digestion, random shearing orrestriction enzyme digestion. The concentration of nucleic acidfragments of a particular length or sequence is often less than 0.1 % or1% by weight of the total nucleic acid. The number of different specificnucleic acid fragments in the mixture is usually at least about 100, 500or 1000.

The mixed population of nucleic acid fragments are denatured by heatingto about 80° C. to 100° C., more preferably from 90° C. to 96° C., toform single-stranded nucleic acid fragments and then reannealed.Single-stranded nucleic acid fragments having regions of sequenceidentity with other single-stranded nucleic acid fragments can then bereannealed by cooling to 20° C. to 75° C., and preferably from 40° C. to65° C. Renaturation can be accelerated by the addition of polyethyleneglycol (“PEG”) or salt. The salt concentration is preferably from 0 mMto 600 mM, more preferably the salt concentration is from 10 mM to 100mM. The salt may be such salts as (NH₄)₂SO₄, KCl, or NaCl. Theconcentration of PEG is preferably from 0% to 20%, more preferably from5% to 10%. The fragments that reanneal can be from different substratesas shown in FIG. 1, panel C.

The annealed nucleic acid fragments are incubated in the presence of anucleic acid polymerase, such as Taq or Klenow, and dNTP's (i.e. dATP,dCTP, dGTP and dTTP). If regions of sequence identity are large, Taq orother high-temperature polymerase can be used with an annealingtemperature of between 45-65° C. If the areas of identity are small,Klenow or other low-temperature polymerases can be used with anannealing temperature of between 20-30° C. The polymerase can be addedto the random nucleic acid fragments prior to annealing, simultaneouslywith annealing or after annealing.

The cycle of denaturation, renaturation and incubation of random nucleicacid fragments in the presence of polymerase is sometimes referred to as“shuffling” of the nucleic acid in vitro. This cycle is repeated for adesired number of times. Preferably the cycle is repeated from 2 to 100times, more preferably the sequence is repeated from 10 to 40 times. Theresulting nucleic acids are a family of double-stranded polynucleotidesof from about 50 bp to about 100 kb, preferably from 500 bp to 50 kb, asshown in FIG. 1, panel D. The population represents variants of thestarting substrates showing substantial sequence identity thereto butalso diverging at several positions. The population has many moremembers than the starting substrates. The population of fragmentsresulting from recombination is preferably first amplified by PCR, thencloned into an appropriate vector and the ligation mixture used totransform host cells.

In a variation of in vitro shuffling, subsequences of recombinationsubstrates can be generated by amplifying the full-length sequencesunder conditions which produce a substantial fraction, typically atleast 20 percent or more, of incompletely extended amplificationproducts. The amplification products, including the incompletelyextended amplification products are denatured and subjected to at leastone additional cycle of reannealing and amplification. This variation,wherein at least one cycle of reannealing and amplification provides asubstantial fraction of incompletely extended products, is termed“stuttering.” In the subsequent amplification round, the incompletelyextended products anneal to and prime extension on differentsequence-related template species.

In a further variation, at least one cycle of amplification can beconducted using a collection of overlapping single-stranded DNAfragments of related sequence, and different lengths. Each fragment canhybridize to and prime polynucleotide chain extension of a secondfragment from the collection, thus forming sequence-recombinedpolynucleotides. In a further variation, single-stranded DNA fragmentsof variable length can be generated from a single primer by Vent DNApolymerase on a first DNA template. The single stranded DNA fragmentsare used as primers for a second, Kunkel-type template, consisting of auracil-containing circular single-stranded DNA. This results in multiplesubstitutions of the first template into the second (see Levichkin etal. Mol. Biology 29:572-577 (1995)).

Gene clusters such as those involved in polyketide synthesis (or indeedany multi-enzyme pathways catalyzing analogous metabolic reactions) canbe recombined by recursive sequence recombination even if they lack DNAsequence homology. Homology can be introduced using syntheticoligonucleotides as PCR primers. In addition to the specific sequencesfor the gene being amplified, all of the primers used to amplify onetype of enzyme (for example the acyl carrier protein in polyketidesynthesis) are synthesized to contain an additional sequence of 20-40bases 5′ to the gene (sequence A) and a different 20-40 base sequence 3′to the gene (sequence B). The adjacent gene (in this case theketo-synthase) is amplified using a 5′ primer which contains thecomplementary strand of sequence B (sequence B′), and a 3′ primercontaining a different 20-40 base sequence (C). Similarly, primers forthe next adjacent gene (keto-reductases) contain sequences C′(complementary to C) and D. If 5 different polyketide gene clusters arebeing shuffled, all five acyl carrier proteins are flanked by sequencesA and B following their PCR amplification. In this way, small regions ofhomology are introduced, making the gene clusters into site-specificrecombination cassettes. Subsequent to the initial amplification ofindividual genes, the amplified genes S can then be mixed and subjectedto primerless PCR. Sequence B at the 3′ end of all of the five acylcarrier protein genes can anneal with and prime DNA synthesis fromsequence B′ at the 5′ end of all five keto reductase genes. In this wayall possible combinations of genes within the cluster can be obtained.Oligonucleotides allow such recombinants to be obtained in the absenceof sufficient sequence homology for recursive sequence recombinationdescribed above. Only homology of function is required to producefunctional gene clusters.

This method is also useful for exploring permutations of any othermulti-subunit enzymes. An example of such enzymes composed of multiplepolypeptides that have shown novel functions when the subunits arecombined in novel ways are dioxygenases. Directed recombination betweenthe four protein subunits of biphenyl and toluene dioxygenases producedfunctional dioxygenases with increased activity againsttrichloroethylene (Furukawa et. al. J. Bacteriol. 176: 2121-2123(1994)). This combination of subunits from the two dioxygenases couldalso have been produced by cassette-shuffling of the dioxygenases asdescribed above, followed by selection for degradation oftrichloroethylene.

In some polyketide synthases, the separate functions of the acyl carrierprotein, keto-synthase, keto-reductase, etc. reside in a singlepolypeptide. In these cases domains within the single polypeptide may beshuffled, even if sufficient homology does not-exist naturally, byintroducing regions of homology as described above for entire genes. Inthis case, it may not be possible to introduce additional flankingsequences to the domains, due to the constraint of maintaining acontinuous open reading frame. Instead, groups of oligonucleotides aresynthesized that are homologous to the 3′ end of the first domainencoded by one of the genes to be shuffled, and the 5′ ends of thesecond domains encoded by all of the other genes to be shuffledtogether. This is repeated with all domains, thus providing sequencesthat allow recombination between protein domains while maintaining theirorder.

The cassette-based recombination method can be combined with recursivesequence recombination by including gene fragments (generated by DNase,physical shearing, DNA stuttering, etc.) for one or more of the genes.Thus, in addition to different combinations of entire genes within acluster (e.g., for polyketide synthesis), individual genes can beshuffled at the same time (e.g., all acyl carrier protein genes can alsobe provided as fragmented DNA), allowing a more thorough search ofsequence space.

(2) In Vivo Formats

(a) Plasmid-Plasmid Recombination

The initial substrates for recombination are a collection ofpolynucleotides comprising variant forms of a gene. The variant formsusually show substantial sequence identity to each other sufficient toallow homologous recombination between substrates. The diversity betweenthe polynucleotides can be natural (e.g., allelic or species variants),induced (e.g., error-prone PCR or error-prone recursive sequencerecombination), or the result of in vitro recombination. Diversity canalso result from resynthesizing genes encoding natural proteins withalternative codon usage. There should be at least sufficient diversitybetween substrates that recombination can generate more diverse productsthan there are starting materials. There must be at least two substratesdiffering in at least two positions. However, commonly a library ofsubstrates of 10³-10⁸ members is employed. The degree of diversitydepends on the length of the substrate being recombined and the extentof the functional change to be evolved. Diversity at between 0.1-25% ofpositions is typical. The diverse substrates are incorporated intoplasmids. The plasmids are often standard cloning vectors, e.g.,bacterial multicopy plasmids. However, in some methods to be describedbelow, the plasmids include mobilization (MOB) functions. The substratescan be incorporated into the same or different plasmids. Often at leasttwo different types of plasmid having different types of selectablemarkers are used to allow selection for cells containing at least twotypes of vector. Also, where different types of plasmid are employed,the different plasmids can come from two distinct incompatibility groupsto allow stable co-existence of two different plasmids within the cell.Nevertheless, plasmids from the same incompatibility group can stillco-exist within the same cell for sufficient time to allow homologousrecombination to occur.

Plasmids containing diverse substrates are initially introduced intocells by any method (e.g., chemical transformation, natural competence,electroporation, biolistics, packaging into phage or viral systems).Often, the plasmids are present at or near saturating concentration(with respect to maximum transfection capacity) to increase theprobability of more than one plasmid entering the same cell. Theplasmids containing the various substrates can be transfectedsimultaneously or in multiple rounds. For example, in the latterapproach cells can be transfected with a first aliquot of plasmid,transfectants selected and propagated, and then infected with a secondaliquot of plasmid.

Having introduced the plasmids into cells, recombination betweensubstrates to generate recombinant genes occurs within cells containingmultiple different plasmids merely by propagating the cells. However,cells that receive only one plasmid are unable to participate inrecombination and the potential contribution of substrates on suchplasmids to evolution is not fully exploited (although these plasmidsmay contribute to some extent if they are propagated in mutator cells).The rate of evolution can be increased by allowing all substrates toparticipate in recombination. Such can be achieved by subjectingtransfected cells to electroporation. The conditions for electroporationare the same as those conventionally used for introducing exogenous DNAinto cells (e.g., 1,000-2,500 volts, 400 μF and a 1-2 mM gap). Underthese conditions, plasmids are exchanged between cells allowing allsubstrates to participate in recombination. In addition the products ofrecombination can undergo further rounds of recombination with eachother or with the original substrate. The rate of evolution can also beincreased by use of conjugative transfer. To exploit conjugativetransfer, substrates can be cloned into plasmids having MOB genes, andtra genes are also provided in cis or in trans to the MOB genes. Theeffect of conjugative transfer is very similar to electroporation inthat it allows plasmids to move between cells and allows recombinationbetween any substrate and the products of previous recombination tooccur, merely by propagating the culture. The rate of evolution can alsobe increased by fusing cells to induce exchange of plasmids orchromosomes. Fusion can be induced by chemical agents, such as PEG, orviral proteins, such as influenza virus hemagglutinin, HSV-1 gB and gD.The rate of evolution can also be increased by use of mutator host cells(e.g., Mut L, S, D, T, H in bacteria and Ataxia telangiectasia humancell lines).

The time for which cells are propagated and recombination is allowed tooccur, of course, varies with the cell type but is generally notcritical, because even a small degree of recombination can substantiallyincrease diversity relative to the starting materials. Cells bearingplasmids containing recombined genes are subject to screening orselection for a desired function. For example, if the substrate beingevolved contains a drug resistance gene, one would select for drugresistance. Cells surviving screening or selection can be subjected toone or more rounds of screening/selection followed by recombination orcan be subjected directly to an additional round of recombination.

The next round of recombination can be achieved by several differentformats independently of the previous round. For example, a furtherround of recombination can be effected simply by resuming theelectroporation or conjugation-mediated intercellular transfer ofplasmids described above. Alternatively, a fresh substrate orsubstrates, the same or different from previous substrates, can betransfected into cells surviving selection/screening. Optionally, thenew substrates are included in plasmid vectors bearing a differentselective marker and/or from a different incompatibility group than theoriginal plasmids. As a further alternative, cells survivingselection/screening can be subdivided into two subpopulations, andplasmid DNA from one subpopulation transfected into the other, where thesubstrates from the plasmids from the two subpopulations undergo afurther round of recombination. In either of the latter two options, therate of evolution can be increased by employing DNA extraction,electroporation, conjugation or mutator cells, as described above. In astill further variation, DNA from cells surviving screening/selectioncan be extracted and subjected to in vitro recursive sequencerecombination.

After the second round of recombination, a second round ofscreening/selection is performed, preferably under conditions ofincreased stringency. If desired, further rounds of recombination andselection/screening can be performed using the same strategy as for thesecond round. With successive rounds of recombination andselection/screening, the surviving recombined substrates evolve towardacquisition of a desired phenotype. Typically, in this and other methodsof recursive recombination, the final product of recombination that hasacquired the desired phenotype differs from starting substrates at0.10%-25% of positions and has evolved at a rate orders of magnitude inexcess (e.g., by at least 10-fold, 100-fold, 1000-fold, or 10,000 fold)of the rate of naturally acquired mutation of about 1 mutation per 10⁻⁹positions per generation (see Andersson et al. Proc. Natl. Acad. Sci.U.S.A. 93:906-907 (1996)). The “final product” may be transferred toanother host more desirable for utilization of the “shuffled” DNA. Thisis particularly advantageous in situations where the more desirable hostis less efficient as a host for the many cycles ofmutation/recombination due to the lack of molecular biology or genetictools available for other organisms such as E. coli.

(b) Virus-Plasmid Recombination

The strategy used for plasmid-plasmid recombination can also be used forvirus-plasmid recombination; usually, phage-plasmid recombination.However, some additional comments particular to the use of viruses areappropriate. The initial substrates for recombination are cloned intoboth plasmid and viral vectors. It is usually not critical whichsubstrate(s) are inserted into the viral vector and which into theplasmid, although usually the viral vector should contain differentsubstrate(s) from the plasmid. As before, the plasmid (and the virus)typically contains a selective marker. The plasmid and viral vectors canboth be introduced into cells by transfection as described above.However, a more efficient procedure is to transfect the cells withplasmid, select transfectants and infect the transfectants with virus.Because the efficiency of infection of many viruses approaches 100% ofcells, most cells transfected and infected by this route contain both aplasmid and virus bearing different substrates.

Homologous recombination occurs between plasmid and virus generatingboth recombined plasmids and recombined virus. For some viruses, such asfilamentous phage, in which intracellular DNA exists in bothdouble-stranded and single-stranded forms, both can participate inrecombination. Provided that the virus is not one that rapidly killscells, recombination can be augmented by use of electroporation orconjugation to transfer plasmids between cells. Recombination can alsobe augmented for some types of virus by allowing the progeny virus fromone cell to reinfect other cells. For some types of virus, virusinfected-cells show resistance to superinfection. However, suchresistance can be overcome by infecting at high multiplicity and/orusing mutant strains of the virus in which resistance to superinfectionis reduced.

The result of infecting plasmid-containing cells with virus depends onthe nature of the virus. Some viruses, such as filamentous phage, stablyexist with a plasmid in the cell and also extrude progeny phage from thecell. Other viruses, such as lambda having a cosmid genome, stably existin a cell like plasmids without producing progeny virions. Otherviruses, such as the T-phage and lytic lambda, undergo recombinationwith the plasmid but ultimately kill the host cell and destroy plasmidDNA. For viruses that infect cells without killing the host, cellscontaining recombinant plasmids and virus can be screened/selected usingthe same approach as for plasmid-plasmid recombination. Progeny virusextruded by cells surviving selection/screening can also be collectedand used as substrates in subsequent rounds of recombination. Forviruses that kill their host cells, recombinant genes resulting fromrecombination reside only in the progeny virus. If the screening orselective assay requires expression of recombinant genes in a cell, therecombinant genes should be transferred from the progeny virus toanother vector, e.g., a plasmid vector, and retransfected into cellsbefore selection/screening is performed.

For filamentous phage, the products of recombination are present in bothcells surviving recombination and in phage extruded from these cells.The dual source of recombinant products provides some additional optionsrelative to the plasmid-plasmid recombination. For example, DNA can beisolated from phage particles for use in a round of in vitrorecombination. Alternatively, the progeny phage can be used to transfector infect cells surviving a previous round of screening/selection, orfresh cells transfected with fresh substrates for recombination.

(c) Virus-Virus Recombination

The principles described for plasmid-plasmid and plasmid-viralrecombination can be applied to virus-virus recombination with a fewmodifications. The initial substrates for recombination are cloned intoa viral vector. Usually, the same vector is used for all substrates.Preferably, the virus is one that, naturally or as a result of mutation,does not kill cells. After insertion, some viral genomes can be packagedin vitro or using a packaging cell line. The packaged viruses are usedto infect cells at high multiplicity such that there is a highprobability that a cell will receive multiple viruses bearing differentsubstrates.

After the initial round of infection, subsequent steps depend on thenature of infection as discussed in the previous section. For example,if the viruses have phagemid genomes such as lambda cosmids or M13, Flor Fd phagemids, the phagemids behave as plasmids within the cell andundergo recombination simply by propagating the cells. Recombination isparticularly efficient between single-stranded forms of intracellularDNA. Recombination can be augmented by electroporation of cells.

Following selection/screening, cosmids containing recombinant genes canbe recovered from surviving cells, e.g., by heat induction of a cos⁻lysogenic host cell, or extraction of DNA by standard procedures,followed by repackaging cosmid DNA in vitro.

If the viruses are filamentous phage, recombination of replicating formDNA occurs by propagating the culture of infected cells.Selection/screening identifies colonies of cells containing viralvectors having recombinant genes with improved properties, together withphage extruded from such cells. Subsequent options are essentially thesame as for plasmid-viral recombination.

(d) Chromosome Recombination

This format can be used to especially evolve chromosomal substrates. Theformat is particularly useful in situations in which many chromosomalgenes contribute to a phenotype or one does not know the exact locationof the chromosomal gene(s) to be evolved. The initial substrates forrecombination are cloned into a plasmid vector. If the chromosomalgene(s) to be evolved are known, the substrates constitute a family ofsequences showing a high degree of sequence identity but some divergencefrom the chromosomal gene. If the chromosomal genes to be evolved havenot been located, the initial substrates usually constitute a library ofDNA segments of which only a small number show sequence identity to thegene or gene(s) to be evolved. Divergence between plasmid-bornesubstrate and the chromosomal gene(s) can be induced by mutagenesis orby obtaining the plasmid-borne substrates from a different species thanthat of the cells bearing the chromosome.

The plasmids bearing substrates for recombination are transfected intocells having chromosomal gene(s) to be evolved. Evolution can occursimply by propagating the culture, and can be accelerated bytransferring plasmids between cells by conjugation or electroporation.Evolution can be further accelerated by use of mutator host cells or byseeding a culture of nonmutator host cells being evolved with mutatorhost cells and inducing intercellular transfer of plasmids byelectroporation or conjugation. Preferably, mutator host cells used forseeding contain a negative selectable marker to facilitate isolation ofa pure culture of the nonmutator cells being evolved.Selection/screening identifies cells bearing chromosomes and/or plasmidsthat have evolved toward acquisition of a desired function.

Subsequent rounds of recombination and selection/screening proceed insimilar fashion to those described for plasmid-plasmid recombination.For example, further recombination can be effected by propagating cellssurviving recombination in combination with electroporation orconjugative transfer of plasmids. Alternatively, plasmids bearingadditional substrates for recombination can be introduced into thesurviving cells. Preferably, such plasmids are from a differentincompatibility group and bear a different selective marker than theoriginal plasmids to allow selection for cells containing at least twodifferent plasmids. As a further alternative, plasmid and/or chromosomalDNA can be isolated from a subpopulation of surviving cells andtransfected into a second subpopulation. Chromosomal DNA can be clonedinto a plasmid vector before transfection.

(e) Virus-Chromosome Recombination

As in the other methods described above, the virus is usually one thatdoes not kill the cells, and is often a phage or phagemid. The procedureis substantially the same as for plasmid-chromosome recombination.Substrates for recombination are cloned into the vector. Vectorsincluding the substrates can then be transfected into cells or in vitropackaged and introduced into cells by infection. Viral genomes recombinewith host chromosomes merely by propagating a culture. Evolution can beaccelerated by allowing intercellular transfer of viral genomes byelectroporation, or reinfection of cells by progeny virions.Screening/selection identifies cells having chromosomes and/or viralgenomes that have evolved toward acquisition of a desired function.

There are several options for subsequent rounds of recombination. Forexample, viral genomes can be transferred between cells survivingselection/recombination by electroporation. Alternatively, virusesextruded from cells surviving selection/screening can be pooled and usedto superinfect the cells at high multiplicity. Alternatively, freshsubstrates for recombination can be introduced into the cells, either onplasmid or viral vectors.

II. Recursive Sequence Recombination Techniques for Metabolic andCellular Engineering

A. Starting Materials

Thus, a general method for recursive sequence recombination for theembodiments herein is to begin with a gene encoding an enzyme or enzymesubunit and to evolve that gene either for ability to act on a newsubstrate, or for enhanced catalytic properties with an old substrate,either alone or in combination with other genes in a multistep pathway.The term “gene” is used herein broadly to refer to any segment orsequence of DNA associated with a biological function. Genes can beobtained from a variety of sources, including cloning from a source ofinterest or synthesizing from known or predicted sequenceinformation,and may include sequences designed to have desiredparameters. The ability to use a new substrate can be assayed in someinstances by the ability to grow on a substrate as a nutrient source. Inother circumstances such ability can be assayed by decreased toxicity ofa substrate for a host cell, hence allowing the host to grow in thepresence of that substrate. Biosynthesis of new compounds, such asantibiotics, can be assayed similarly by growth of an indicator organismin the presence of the host expressing the evolved genes. For example,when an indicator organism used in an overlay of the host expressing theevolved gene(s), wherein the indicator organism is sensitive or expectedto be sensitive to the desired antibiotic, growth of the indicatororganism would be inhibited in a zone around the host cell or colonyexpressing the evolved gene(s).

Another method of identifying new compounds is the use of standardanalytical techniques such as mass spectroscopy, nuclear magneticresonance, high performance liquid chromatography, etc. Recombinantmicroorganisms can be pooled and extracts or media supernatants assayedfrom these pools. Any positive pool can then be subdivided and theprocedure repeated until the single positive is identified(“sib-selection”).

In some instances, the starting material for recursive sequencerecombination is a discrete gene, cluster of genes, or family of genesknown or thought to be associated with metabolism of a particular classof substrates.

One of the advantages of the instant invention is that structuralinformation is not required to estimate which parts of a sequence shouldbe mutated to produce a functional hybrid enzyme.

In some embodiments of the invention, an initial screening of enzymeactivities in a particular assay can be useful in identifying candidateenzymes as starting materials. For example, high throughput screeningcan be used to screen enzymes for dioxygenase-type activities usingaromatic acids as substrates. Dioxygenases typically transformindole-2-carboxylate and indole-3-carboxylate to colored products,including indigo (Eaton et. al. J. Bacteriol. 177:6983-6988 (1995)). DNAencoding enzymes that give some activity in the initial assay can thenbe recombined by the recursive techniques of the invention andrescreened. The use of such initial screening for candidate enzymesagainst a desired target molecule or analog of the target molecule canbe especially useful to generate enzymes that catalyze reactions ofinterest such as catabolism of man-made pollutants.

The starting material can also be a segment of such a gene or clusterthat is recombined in isolation of its surrounding DNA, but is relinkedto its surrounding DNA before screening/selection of recombinationproducts. In other instances, the starting material for recombination isa larger segment of DNA that includes a coding sequence or other locusassociated with metabolism of a particular substrate at an unknownlocation. For example, the starting material can be a chromosome,episome, YAC, cosmid, or phage P1 clone. In still other instances, thestarting material is the whole genome of an organism that is known tohave desirable metabolic properties, but for which no informationlocalizing the genes associated with these characteristics is available.

In general any type of cells can be used as a recipient of evolvedgenes. Cells of particular interest include many bacterial cell types,both gram-negative and gram-positive, such as Rhodococcus,Streptomycetes, Actinomycetes, Corynebacteria, Penicillium, Bacillus,Escherichia coli, Pseudomonas, Salmonella, and Erwinia. Cells ofinterest also include eukaryotic cells, particularly mammalian cells(e.g., mouse, hamster, primate, human), both cell lines and primarycultures. Such cells include stem cells, including embryonic stem cells,zygotes, fibroblasts, lymphocytes, Chinese hamster ovary (CHO), mousefibroblasts (NIH3T3), kidney, liver, muscle, and skin cells. Othereukaryotic cells of interest include plant cells, such as maize, rice,wheat, cotton, soybean, sugarcane, tobacco, and arabidopsis; fish,algae, fungi (Penicillium, Fusarium, Aspergillus, Podospora,Neurospora), insects, yeasts (Picchia and Saccharomyces).

The choice of host will depend on a number of factors, depending on theintended use of the engineered host, including pathogenicity, substraterange, environmental hardiness, presence of key intermediates, ease ofgenetic manipulation, and likelihood of promiscuous transfer of geneticinformation to other organisms. Particularly advantageous hosts are E.coli, lactobacilli, Streptomycetes, Actinomycetes and filamentous fungi.

The breeding procedure starts with at least two substrates, whichgenerally show substantial sequence identity to each other (i.e., atleast about 50%, 70%, 80% or 90% sequence identity) but differ from eachother at certain positions. The difference can be any type of mutation,for example, substitutions, insertions and deletions. Often, differentsegments differ from each other in perhaps 5-20 positions. Forrecombination to generate increased diversity relative to the startingmaterials, the starting materials must differ from each other in atleast two nucleotide positions. That is, if there are only twosubstrates, there should be at least two divergent positions. If thereare three substrates, for example, one substrate can differ from thesecond as a single position, and the second can differ from the third ata different single position. The starting DNA segments can be naturalvariants of each other, for example, allelic or species variants. Thesegments can also be from nonallelic genes showing some degree ofstructural and usually functional relatedness (e.g., different geneswithin a superfamily such as the immunoglobulin superfamily). Thestarting DNA segments can also be induced variants of each other. Forexample, one DNA segment can be produced by error-prone PCR replicationof the other, or by substitution of a mutagenic cassette. Inducedmutants can also be prepared by propagating one (or both) of thesegments in a mutagenic strain. In these situations, strictly speaking,the second DNA segment is not a single segment but a large family ofrelated segments. The different segments forming the starting materialsare often the same length or substantially the same length. However,this need not be the case; for example; one segment can be a subsequenceof another. The segments can be present as part of larger molecules,such as vectors, or can be in isolated form.

The starting DNA segments are recombined by any of the recursivesequence recombination formats described above to generate a diverselibrary of recombinant DNA segments. Such a library can vary widely insize from having fewer than 10 to more than 10⁵, 10⁷, or 10⁹ members. Ingeneral, the starting segments and the recombinant libraries generatedinclude full-length coding sequences and any essential regulatorysequences, such as a promoter and polyadenylation sequence, required forexpression. However, if this is not the case, the recombinant DNAsegments in the library can be inserted into a common vector providingthe missing sequences before performing screening/selection.

If the recursive sequence recombination format employed is an in vivoformat, the library of recombinant DNA segments generated already existsin a cell, which is usually the cell type in which expression of theenzyme with altered substrate specificity is desired. If recursivesequence recombination is performed in vitro, the recombinant library ispreferably introduced into the desired cell type beforescreening/selection. The members of the recombinant library can belinked to an episome or virus before introduction or. can be introduceddirectly. In some embodiments of the invention, the library is amplifiedin a first host, and is then recovered from that host and introduced toa second host more amenable to expression, selection, or screening, orany other desirable parameter. The manner in which the library isintroduced into the cell type depends on the DNA-uptake characteristicsof the cell type, e.g., having viral receptors, being capable ofconjugation, or being naturally competent. If the cell type isinsusceptible to natural and chemical-induced competence, butsusceptible to electroporation, one would usually employelectroporation. If the cell type is insusceptible to electroporation aswell, one can employ biolistics. The biolistic PDS-1000 Gene Gun(Biorad, Hercules, Calif.) uses helium pressure to accelerate DNA-coatedgold or tungsten microcarriers toward target cells. The process isapplicable to a wide range of tissues, including plants, bacteria,fungi, algae, intact animal tissues, tissue culture cells, and animalembryos. One can employ electronic pulse delivery, which is essentiallya mild electroporation format for live tissues in animals and patients.Zhao, Advanced Drug Delivery Reviews 17:257-262 (1995). Novel methodsfor making cells competent are described in co-pending application U.S.patent application Ser. No. 08/621,430, filed Mar. 25, 1996. Afterintroduction of the library of recombinant DNA genes, the cells areoptionally propagated to allow expression of genes to occur.

B. Selection and Screening

Screening is, in general, a two-step process in which one firstdetermines which cells do and do not express a screening marker and thenphysically separates the cells having the desired property. Selection isa form of screening in which identification and physical separation areachieved simultaneously, for example, by expression of a selectablemarker, which, in some genetic circumstances, allows cells expressingthe marker to survive while other cells die (or vice versa). Screeningmarkers include, for example, luciferase, β-galactosidase, and greenfluorescent protein. Screening can also be done by observing suchaspects of growth as colony size, halo formation, etc. Additionally,screening for production of a desired compound, such as a therapeuticdrug or “designer chemical” can be accomplished by observing binding ofcell products to a receptor or ligand, such as on a solid support or ona column. Such screening can additionally be accomplished by binding toantibodies, as in an ELISA. In some instances the screening process ispreferably automated so as to allow screening of suitable numbers ofcolonies or cells. Some examples of automated screening devices includefluorescence activated cell sorting, especially in conjunction withcells immobilized in agarose (see Powell et. al. Bio/Technoloqy8:333-337 (1990); Weaver et. al. Methods 2:234-247 (1991)), automatedELISA assays, etc. Selectable markers can include, for example, drug,toxin resistance, or nutrient synthesis genes. Selection is also done bysuch techniques as growth on a toxic substrate to select for hostshaving the ability to detoxify a substrate, growth on a new nutrientsource to select for hosts having the ability to utilize that nutrientsource, competitive growth in culture based on ability to utilize anutrient source, etc.

In particular, uncloned but differentially expressed proteins (e.g.,those induced in response to new compounds, such as biodegradablepollutants in the medium) can be screened by differential display(Appleyard et al. Mol. Gen. Gent. 247:338-342 (1995)). Hopwood (PhilTrans R. Soc. Lond B 324:549-562) provides a review of screens forantibiotic production. Omura (Microbio. Rev. 50:259-279 (1986) andNisbet (Ann Rep. Med. Chem. 21:149-157 (1986)) disclose screens forantimicrobial agents, including supersensitive bacteria, detection ofβ-lactamase and D,D-carboxypeptidase inhibition, β-lactamase induction,chromogenic substrates and monoclonal antibody screens. Antibiotictargets can also be used as screening targets in high throughputscreening. Antifungals are typically screened by inhibition of fungalgrowth. Pharmacological agents can be identified as enzyme inhibitorsusing plates containing the enzyme and a chromogenic substrate, or byautomated receptor assays. Hydrolytic enzymes (e.g., proteases,amylases) can be screened by including the substrate in an agar plateand scoring for a hydrolytic clear zone or by using a calorimetricindicator (Steele et al. Ann. Rev. Microbiol. 45:89-106 (1991)). Thiscan be coupled with the use of stains to detect the effects of enzymeaction (such as congo red to detect the extent of degradation ofcelluloses and hemicelluloses). Tagged substrates can also be used. Forexample, lipases and esterases can be screened using different lengthsof fatty acids linked to umbelliferyl. The action of lipases oresterases removes this tag from the fatty acid, resulting in a quenchingof umbelliferyl fluorescence. These enzymes can be screened inmicrotiter plates by a robotic device.

Fluorescence activated cell sorting (FACS) methods are also a powerfultool for selection/screening. In some instances a fluorescent moleculeis made within a cell (e.g., green fluorescent protein). The cellsproducing the protein can simply be sorted by FACS. Gel microdroptechnology allows screening of cells encapsulated in agarose microdrops(Weaver et al. Methods 2:234-247 (1991)). In this technique productssecreted by the cell (such as antibodies or antigens) are immobilizedwith the cell that generated them. Sorting and collection of the dropscontaining the desired product thus also collects the cells that madethe product, and provides a ready source for the cloning of the genesencoding the desired functions. Desired products can be detected byincubating the encapsulated cells with fluorescent antibodies (Powell etal. Bio/Technology 8:333-337 (1990)). FACS sorting can also be used bythis technique to assay resistance to toxic compounds and antibiotics byselecting droplets that contain multiple cells (i.e., the product ofcontinued division in the presence of a cytotoxic compound; Goguen etal. Nature 363:189-190 (1995)). This method can select for any enzymethat can change the fluorescence of a substrate that can be immobilizedin the agarose droplet.

In some embodiments of the invention, screening can be accomplished byassaying reactivity with a reporter molecule reactive with a desiredfeature of, for example, a gene product. Thus, specific functionalitiessuch as antigenic domains can be screened with antibodies specific forthose determinants.

In other embodiments of the invention, screening is preferably done witha cell-cell indicator assay. In this assay format, separate librarycells (Cell A, the cell being assayed) and reporter cells (Cell B, theassay cell) are used. Only one component of the system, the librarycells, is allowed to evolve. The screening is generally carried out in atwo-dimensional immobilized format, such as on plates. The products ofthe metabolic pathways encoded by these genes (in this case, usuallysecondary metabolites such as antibiotics, polyketides, carotenoids,etc.) diffuse out of the library cell to the reporter cell. The productof the library cell may affect the reporter cell in one of a number ofways.

The assay system (indicator cell) can have a simple readout (e.g., greenfluorescent protein, luciferase, β-galactosidase) which is induced bythe library cell product but which does not affect the library cell. Inthese examples the desired product can be detected by calorimetricchanges in the reporter cells adjacent to the library cell.

In other embodiments, indicator cells can in turn produce something thatmodifies the growth rate of the library cells via a feedback mechanism.Growth rate feedback can detect and accumulate very small differences.For example, if the library and reporter cells are competing fornutrients, library cells producing compounds to inhibit the growth ofthe reporter cells will have more available nutrients, and thus willhave more opportunity for growth. This is a useful screen forantibiotics or a library of polyketide synthesis gene clusters whereeach of the library cells is expressing and exporting a differentpolyketide gene product.

Another variation of this theme is that the reporter cell for anantibiotic selection can itself secrete a toxin or antibiotic thatinhibits growth of the library cell. Production by the library cell ofan antibiotic that is able to suppress growth of the reporter cell willthus allow uninhibited growth of the library cell.

Conversely, if the library is being screened for production of acompound that stimulates the growth of the reporter cell (for example,in improving chemical syntheses, the library cell may supply nutrientssuch as amino acids to an auxotrophic reporter, or growth factors to agrowth-factor-dependent reporter. The reporter cell in turn shouldproduce a compound that stimulates the growth of the library cell.Interleukins, growth factors, and nutrients are possibilities.

Further possibilities include competition based on ability to killsurrounding cells, positive feedback loops in which the desired productmade by the evolved cell stimulates the indicator cell to produce apositive growth factor for cell A, thus indirectly selecting forincreased product formation.

In some embodiments of the invention it can be advantageous to use adifferent organism (or genetic background) for screening than the onethat will be used in the final product. For example, markers can beadded to DNA constructs used for recursive sequence recombination tomake the microorganism dependent on the constructs during theimprovement process, even though those markers may be undesirable in thefinal recombinant microorganism.

Likewise, in some embodiments it is advantageous to use a differentsubstrate for screening an evolved enzyme than the one that will be usedin the final product. For example, Evnin et al. (Proc. Natl. Acad. Sci.U.S.A. 87:6659-6663 (1990)) selected trypsin variants with alteredsubstrate specificity by requiring that variant trypsin generate anessential amino acid for an arginine auxotroph by cleaving arginineβ-naphthylamide. This is thus a selection for arginine-specific trypsin,with the growth rate of the host being proportional to that of theenzyme activity.

The pool of cells surviving screening and/or selection is enriched forrecombinant genes conferring the desired phenotype (e.g. alteredsubstrate specificity, altered biosynthetic ability, etc.). Furtherenrichment can be obtained, if desired, by performing a second round ofscreening and/or selection without generating additional diversity.

The recombinant gene or pool of such genes surviving one round ofscreening/selection forms one or more of the substrates for a secondround of recombination. Again, recombination can be performed in vivo orin vitro by any of the recursive sequence recombination formatsdescribed above. If recursive sequence recombination is performed invitro, the recombinant gene or genes to form the substrate forrecombination should be extracted from the cells in whichscreening/selection was performed. Optionally, a subsequence of suchgene or genes can be excised for more targeted subsequent recombination.If the recombinant gene(s) are contained within episomes, theirisolation presents no difficulties. If the recombinant genes arechromosomally integrated, they can be isolated by amplification primedfrom known sequences flanking the regions in which recombination hasoccurred. Alternatively, whole genomic DNA can be isolated, optionallyamplified, and used as the substrate for recombination. Small samples ofgenomic DNA can be amplified by whole genome amplification withdegenerate primers (Barrett et al. Nucleic Acids Research 23:3488-3492(1995)). These primers result in a large amount of random 3′ ends, whichcan undergo homologous recombination when reintroduced into cells.

If the second round of recombination is to be performed in vivo, as isoften the case, it can be performed in the cell survivingscreening/selection, or the recombinant genes can be transferred toanother cell type (e.g., a cell type having a high frequency of mutationand/or recombination). In this situation, recombination can be effectedby introducing additional DNA segment(s) into cells bearing therecombinant genes. In other methods, the cells can be induced toexchange genetic information with each other by, for example,electroporation. In some methods, the second round of recombination isperformed by dividing a pool of cells surviving screening/selection inthe first round into two subpopulations. DNA from one subpopulation isisolated and transfected into the other population, where therecombinant gene(s) from the two subpopulations recombine to form afurther library of recombinant genes. In these methods, it is notnecessary to isolate particular genes from the first subpopulation or totake steps to avoid random shearing of DNA during extraction. Rather,the whole genome of DNA sheared or otherwise cleaved into manageablesized fragments is transfected into the second subpopulation. Thisapproach is particularly useful when several genes are being evolvedsimultaneously and/or the location and identity of such genes withinchromosome are not known.

The second round of recombination is sometimes performed exclusivelyamong the recombinant molecules surviving selection. However, in otherembodiments, additional substrates can be introduced. The additionalsubstrates can be of the same form as the substrates used in the firstround of recombination, i.e., additional natural or induced mutants ofthe gene or cluster of genes, forming the substrates for the firstround. Alternatively, the additional substrate(s) in the second round ofrecombination can be exactly the same as the substrate(s) in the firstround of replication.

After the second round of recombination, recombinant genes conferringthe desired phenotype are again selected. The selection process proceedsessentially as before. If a suicide vector bearing a selective markerwas used in the first round of selection, the same vector can be usedagain. Again, a cell or pool of cells surviving selection is selected.If a pool of cells, the cells can be subject to further enrichment.

III. Recursive Sequence Recombination of Genes For Bioremediation

Modern industry generates many pollutants for which the environment canno longer be considered an infinite sink. Naturally occurringmicroorganisms are able to metabolize thousands of organic compounds,including many not found in nature (e.g xenobiotics). Bioremediation,the deliberate use of microorganisms for the biodegradation of man-madewastes, is an emerging technology that offers cost and practicalityadvantages over traditional methods of disposal. The success ofbioremediation depends on the availability of organisms that are able todetoxify or mineralize pollutants. Microorganisms capable of degradingspecific pollutants can be generated by genetic engineering andrecursive sequence recombination.

Although bioremediation is an aspect of pollution control, a more usefulapproach in the long term is one of prevention before industrial wasteis pumped into the environment. Exposure of industrial waste streams torecursive sequence recombination-generated microorganisms capable ofdegrading the pollutants they contain would result in detoxification ofmineralization of these pollutants before the waste stream enters theenvironment. Issues of releasing recombinant organisms can be avoided bycontaining them within bioreactors fitted to the industrial effluentpipes. This approach would also allow the microbial mixture used to beadjusted to best degrade the particular wastes being produced. Finally,this method would avoid the problems of adapting to the outside worldand dealing with competition that face many laboratory microorganisms.

In the wild, microorganisms have evolved new catabolic activitiesenabling them to exploit pollutants as nutrient sources for which thereis no competition. However, pollutants that are present at lowconcentrations in the environment may not provide a sufficient advantageto stimulate the evolution of catabolic enzymes. For a review of suchnaturally occurring evolution of biodegradative pathways and themanipulation of some of microorganisms by classical techniques, seeRamos et al., Bio/Technology 12:1349-1355 (1994).

Generation of new catabolic enzymes or pathways for bioremediation hasthus relied upon deliberate transfer of specific genes between organisms(Wackett et al., supra), forced matings between bacteria with specificcatabolic capabilities (Brenner et al. Biodegradation 5:359-377 (1994)),or prolonged selection in a chemostat. Some researchers have attemptedto facilitate evolution via naturally occurring genetic mechanisms intheir chemostat selections by including microorganisms with a variety ofcatabolic pathways (Kellogg et. al. Science 214:1133-1135 (1981);Chakrabarty American Society of Micro. Biol. News 62:130-137 (1996)).For a review of efforts in this area, see Cameron et al. AppliedBiochem. Biotech. 38:105-140 (1993).

Current efforts in improving organisms for bioremediation take alabor-intensive approach in which many parameters are optimizedindependently, including transcription efficiency from native andheterologous promoters, regulatory circuits and translational efficiencyas well as improvement of protein stability and activity (Timmis et al.Ann. Rev. Microbiol. 48:525-527 (1994)).

A recursive sequence recombination approach overcomes a number oflimitations in the bioremediation capabilities of naturally occurringmicroorganisms. Both enzyme activity and specificity can be altered,simultaneously or sequentially, by the methods of the invention. Forexample, catabolic enzymes can be evolved to increase the rate at whichthey act on a substrate. Although knowledge of a rate-limiting step in ametabolic pathway is not required to practice the invention,rate-limiting proteins in pathways can be evolved to have increasedexpression and/or activity, the requirement for inducing substances canbe eliminated, and enzymes can be evolved that catalyze novel reactions.

Some examples of chemical targets for bioremediation include but are notlimited to benzene, xylene, and toluene, camphor, naphthalene,halogenated hydrocarbons, polychlorinated biphenyls (PCBs),trichlorethylene, pesticides such as pentachlorophenyls (PCPs), andherbicides such as atrazine.

A. Aromatic Hydrocarbons

Preferably, when an enzyme is “evolved” to have a new catalyticfunction, that function is expressed, either constitutively or inresponse to the new substrate. Recursive sequence recombination subjectsboth structural and regulatory elements (including the structure ofregulatory proteins) of a protein to recombinogenic mutagenesissimultaneously. Selection of mutants that are efficiently able to usethe new substrate as a nutrient source will be sufficient to ensure thatboth the enzyme and its regulation are optimized, without detailedanalysis of either protein structure or operon regulation.

Examples of aromatic hydrocarbons include but are not limited tobenzene, xylene, toluene, biphenyl, and polycyclic aromatic hydrocarbonssuch as pyrene and naphthalene. These compounds are metabolized viacatechol intermediates. Degradation of catechol by Pseudomonas putidarequires induction of the catabolic operon by cis, cis-muconate whichacts on the CatR regulatory protein. The binding site for the CatRprotein is G-N₁₁-A, while the optimal sequence for the LysR class ofactivators (of which CatR is a member) is T-N₁₁-A. Mutation of the G toa T in the CatR binding site enhances the expression of catecholmetabolizing genes (Chakrabarty, American Society of Microbiology News62:130-137 (1996)). This demonstrates that the control of existingcatabolic pathways is not optimized for the metabolism of specificxenobiotics. It is also an example of a type of mutant that would beexpected from recursive sequence recombination of the operon followed byselection of bacteria that are better able to degrade the targetcompound.

As an example of starting materials, dioxygenases are required for manypathways in which aromatic compounds are catabolized. Even smalldifferences in dioxygenase sequence can lead to significant differencesin substrate specificity (Furukawa et al. J. Bact. 175:5224-5232 (1993);Erickson et al. App. Environ. Micro. 59:3858-3862 (1993)). A hybridenzyme made using sequences derived from two “parentall” enzymes maypossess catalytic activities that are intermediate between the parents(Erickson, ibid.), or may actually be better than either parent for aspecific reaction (Furukawa et al. J. Bact. 176:2121-2123 (1994)). Inone of these cases site directed mutagenesis was used to generate asingle polypeptide with hybrid sequence (Erickson, ibid.); in the other,a four subunit enzyme was produced by expressing two subunits from eachof two different dioxygenases (Furukawa, ibid.). Thus, sequences fromone or more genes encoding dioxygenases can be used in the recursivesequence recombination techniques of the instant invention, to generateenzymes with new specificities. In addition, other features of thecatabolic pathway can also be evolved using these techniques,simultaneously or sequentially, to optimize the metabolic pathway for anactivity of interest.

B. Halogenated Hydrocarbons

Large quantities of halogenated hydrocarbons are produced annually foruses as solvents and biocides. These include, in the United Statesalone, over 5 million tons of both 1,2-dichloroethane and vinyl chlorideused in PVC production in the U.S. alone. The compounds are largely notbiodegradable by processes in single organisms, although in principlehaloaromatic catabolic pathways can be constructed by combining genesfrom different microorganisms. Enzymes can be manipulated to changetheir substrate specificities. Recursive sequence recombination offersthe possibility of tailoring enzyme specificity to new substrateswithout needing detailed structural analysis of the enzymes.

As an example of possible starting materials for the methods of theinstant invention, Wackett et al. (Nature 368:627-629 (1994)) recentlydemonstrated that through classical techniques a recombinant Pseudomonasstrain in which seven genes encoding two multi-component oxygenases arecombined, generated a single host that can metabolize polyhalogenatedcompounds by sequential reductive and oxidative techniques to yieldnon-toxic products. These and/or related materials can be subjected tothe techniques discussed above so as to evolve and optimize abiodegradative pathway in a single organism.

Trichloroethylene is a significant groundwater contaminant. It isdegraded by microorganisms in a cometabolic way (i.e., no energy ornutrients are derived). The enzyme must be induced by a differentcompound (e.g., Pseudomonas cepacia uses toluene-4-monoxygenase, whichrequires induction by toluene, to destroy trichloroethylene).Furthermore, the degradation pathway involves formation of highlyreactive epoxides that can inactivate the enzyme (Timmis et al. Ann.Rev. Microbiol. 48:525-557 (1994)). The recursive sequence recombinationtechniques of the invention could be used to mutate the enzyme and itsregulatory region such that it is produced constitutively, and is lesssusceptible to epoxide inactivation. In some embodiments of theinvention, selection of hosts constitutively producing the enzyme andless susceptible to the epoxides can be accomplished by demanding growthin the presence of increasing concentrations of trichloroethylene in theabsence of inducing substances.

C. Polychlorinated Biphenyls (PCBs) and Polycyclic Aromatic Hydrocarbons(PAHs)

PCBs and PAHs are families of structurally related compounds that aremajor pollutants at many Superfund sites. Bacteria transformed withplasmids encoding enzymes with broader substrate specificity have beenused commercially. In nature, no known pathways have been generated in asingle host that degrade the larger PAHs or more heavily chlorinatedPCBs. Indeed, often the collaboration of anaerobic and aerobic bacteriaare required for complete metabolism.

Thus, likely sources for starting material for recursive sequencerecombination include identified genes encoding PAH-degrading catabolicpathways on large (20-100KB) plasmids (Sanseverino et al. AppliedEnviron. Micro. 59:1931-1937 (1993); Simon et al. Gene 127:31-37 (1993);Zylstra et al. Annals of the NY Acad. Sci. 721:386-398 (1994)); whilebiphenyl and PCB-metabolizing enzymes are encoded by chromosomal geneclusters, and in a number of cases have been cloned onto plasmids(Hayase et al. J. Bacteriol. 172:1160-1164 (1990); Furukawa et al. Gene98:21-28 (1992); Hofer et al. Gene 144:9-16 (1994)). The materials canbe subjected to the techniques discussed above so as to evolve abiodegradative pathway in a single organism.

Substrate specificity in the PCB pathway largely results from enzymesinvolved in initial dioxygenation reactions, and can be significantlyaltered by mutations in those enzymes (Erickson et al. Applied Environ.Micro. 59:3858-38662 (1993); Furukawa et al. J. Bact. 175:5224-5232(1993). Mineralization of PAHs and PCBs requires that the downstreampathway is able to metabolize the products of the initial reaction(Brenner et al. Biodegradation 5:359-377 (1994)). In this case,recursive sequence recombination of the entire pathway with selectionfor bacteria able to use the PCB or PAH as the sole carbon source willallow production of novel PCB and PAH degrading bacteria.

D. Herbicides

A general method for evolving genes for the catabolism of insolubleherbicides is exemplified as follows for atrazine. Atrazine[2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine] is amoderately persistent herbicide which is frequently detected in groundand surface water at concentrations exceeding the 3 ppb health advisorylevel set by the EPA. Atrazine can be slowly metabolized by aPseudomonas species (Mandelbaum et al. Appl. Environ.Micro. 61:1451-1457(1995)). The enzymes catalyzing the first two steps in atrazinemetabolism by Pseudomonas are encoded by genes AtzA and AtzB (de Souzaet al. Appl. Environ. Micro. 61:3373-3378 (1995)). These genes have beencloned in a 6.8 kb fragment into pUC18 (AtzAB-pUC). E. coli carryingthis plasmid converts atrazine to much more soluble metabolites. It isthus possible to screen for enzyme activity by growing bacteria onplates containing atrazine. The herbicide forms an opaque precipitate inthe plates, but cells containing AtzAB-pU18 secrete atrazine degradingenzymes, leading to a clear halo around those cells or colonies.Typically, the size of the halo and the rate of its formation can beused to assess the level of activity so that picking colonies with thelargest halos allows selection of the more active or highly producedatrazine degrading enzymes. Thus, the plasmids carrying these genes canbe subjected to the recursive sequence recombination formats describedabove to optimize the catabolism of atrazine in E. coli or another hostof choice, including Pseudomonas. After each round of recombination,screening of host colonies expressing the evolved genes can be done onagar plates containing atrazine to observe halo formation. This is agenerally applicable method for screening enzymes that metabolizeinsoluble compounds to those that are soluble (e.g., polycyclicaromatichydrocarbons). Additionally, catabolism of atrazine can provide a sourceof nitrogen for the cell; if no other nitrogen is available, cell growthwill be limited by the rate at which the cells can catabolize nitrogen.Cells able to utilize atrazine as a nitrogen source can thus be selectedfrom a background of non-utilizers or poor-utilizers.

E. Heavy Metal Detoxification

Bacteria are used commercially to detoxify arsenate waste generated bythe mining of arsenopyrite gold ores. As well as mining effluent,industrial waste water is often contaminated with heavy metals (e.g.,those used in the manufacture of electronic components and plastics).Thus, simply to be able to perform other bioremedial functions,microorganisms must be resistant to the levels of heavy metals present,including mercury, arsenate, chromate, cadmium, silver, etc.

A strong selective pressure is the ability to metabolize a toxiccompound to one less toxic. Heavy metals are toxic largely by virtue oftheir ability to denature proteins (Ford et al. Bioextraction andBiodeterioration of Metals, p. 1-23). Detoxification of heavy metalcontamination can be effected in a number of ways including changing thesolubility or bioavailability of the metal, changing its redox state(e.g. toxic mercuric chloride is detoxified by reduction to the muchmore volatile elemental mercury) and even by bioaccumulation of themetal by immobilized bacteria or plants. The accumulation of metals to asufficiently high concentration allows metal to be recycled; smeltingburns off the organic part of the organism, leaving behind reusableaccumulated metal. Resistances to a number of heavy metals (arsenate,cadmium, cobalt, chromium, copper, mercury, nickel, lead, silver, andzinc) are plasmid encoded in a number of species includingStaphylococcus and Pseudomonas (Silver et al. Environ. Health Perspect.102:107-113 (1994); Ji et al. J. Ind. Micro. 14:61-75 (1995)). Thesegenes also confer heavy metal resistance on other species as well (e.g.,E. coli). The recursive sequence recombination techniques of the instantinvention (RSR) can be used to increase microbial heavy metaltolerances, as well as to increase the extent to which cells willaccumulate heavy metals. For example, the ability of E. coli to detoxifyarsenate can be improved at least 100-fold by RSR (see co-pendingapplication Ser. No. 08/621,859, filed Mar. 25, 1996).

Cyanide is very efficiently used to extract gold from rock containing aslittle as 0.2 oz per ton. This cyanide can be microbially neutralizedand used as a nitrogen source by fungi or bacteria such as Pseudomonasfluorescens. A problem with microbial cyanide degradation is thepresence of toxic heavy metals in the leachate. RSR can be used toincrease the resistance of bioremedial microorganisms to toxic heavymetals, so that they will be able to survive the levels present in manyindustrial and Superfund sites. This will allow them to biodegradeorganic pollutants including but not limited to aromatic hydrocarbons,halogenated hydrocarbons, and biocides.

F. Microbial Mining

“Bioleaching” is the process by which microbes convert insoluble metaldeposits (usually metal sulfides or oxides) into soluble metal sulfates.Bioleaching is commercially important in the mining of arsenopyrite, buthas additional potential in the detoxification and recovery of metalsand acids from waste dumps. Naturally occurring bacteria capable ofbioleaching are reviewed by Rawlings and Silver (Bio/Technology13:773-778 (1995)). These bacteria are typically divided into groups bytheir preferred temperatures for growth. The more important mesophilesare Thiobacillus and Leptospirillum species. Moderate thermophilesinclude Sulfobacillus species. Extreme thermophiles include Sulfolobusspecies. Many of these organisms are difficult to grow in commercialindustrial settings, making their catabolic abilities attractivecandidates for transfer to and optimization in other organisms such asPseudomonas, Rhodococcus, T. ferrooxidans or E. coli. Genetic systemsare available for at least one strain of T. ferrooxidans, allowing themanipulation of its genetic material on plasmids.

The recursive sequence recombination methods described above can be usedto optimize the catalytic abilities in native hosts or heterologoushosts for evolved bioleaching genes or pathways, such as the ability toconvert metals from insoluble to soluble salts. In addition, leach ratesof particular ores can be improved as a result of, for example,increased resistance to toxic compounds in the ore concentrate,increased specificity for certain substrates, ability to use differentsubstrates as nutrient sources, and so on.

G. Oil Desulfurization

The presence of sulfur in fossil fuels has been correlated withcorrosion of pipelines, pumping, and refining equipment, and with thepremature breakdown of combustion engines. Sulfur also poisons manycatalysts used in the refining of fossil fuels. The atmospheric emissionof sulfur combustion products is known as acid rain.

Microbial desulfurization is an appealing bioremediation application.Several bacteria have been reported that are capable of catabolizingdibenzothiophene (DBT), which is the representative compound of theclass of sulfur compounds found in fossil fuels. U.S. Pat. No. 5,356,801discloses the cloning of a DNA molecule from Rhodococcus rhodochrouscapable of biocatalyzing the desulfurization of oil. Denome et al. (Gene175:6890-6901 (1995)) disclose the cloning of a 9.8 kb DNA fragment fromPseudomonas encoding the upper naphthalene catabolizing pathway whichalso degrades dibenzothiophene. Other genes have been identified thatperform similar functions (disclosed in U.S. Pat. No. 5,356,801).

The activity of these enzymes is currently too low to be commerciallyviable, but the pathway could be increased in efficiency using therecursive sequence recombination techniques of the invention. Thedesired property of the genes of interest is their ability todesulfurize dibenzothiophene. In some embodiments of the invention,selection is preferably accomplished by coupling this pathway to oneproviding a nutrient to the bacteria. Thus, for example, desulfurizationof dibenzothiophene results in formation of hydroxybiphenyl. This is asubstrate for the biphenyl-catabolizing pathway which provides carbonand energy. Selection would thus be done by “shuffling” thedibenzothiophene genes and transforming them into a host containing thebiphenyl-catabolizing pathway. Increased dibenzothiophenedesulfurization will result in increased nutrient availability andincreased growth rate. Once the genes have been evolved they are easilyseparated from the biphenyl degrading genes. The latter are undesirablein the final product since the object is to desulfurize withoutdecreasing the energy content of the oil.

H. Orcano-Nitro Compounds

Organo-nitro compounds are used as explosives, dyes, drugs, polymers andantimicrobial agents. Biodegradation of these compounds occurs usuallyby way of reduction of the nitrate group, catalyzed by nitroreductases,a family of broadly-specific enzymes. Partial reduction of organo-nitrocompounds often results in the formation of a compound more toxic thanthe original (Hassan et al. 1979 Arch Bioch Biop. 196:385-395).Recursive sequence recombination of nitroreductases can produce enzymesthat are more specific, and able to more completely reduce (and thusdetoxify) their target compounds (examples of which include but are notlimited to nitrotoluenes and nitrobenzenes). Nitro-reductases can beisolated from bacteria isolated from explosive-contaminated soils, suchas Morganella morganii and Enterobacter cloacae (Bryant. et. al., 1991.J. Biol Chem. 266:4126-4130). A preferred selection method is to lookfor increased resistance to the organo-nitro compound of interest, sincethat will indicate that the enzyme is also able to reduce any toxicpartial reduction products of the original compound.

IV. Use of Alternative Substrates for Chemical Synthesis

Metabolic engineering can be used to alter microorganisms that produceindustrially useful chemicals, so that they will grow using alternateand more abundant sources of nutrients, including human-producedindustrial wastes. This typically involves providing both a transportsystem to get the alternative substrate into the engineered cells andcatabolic enzymes from the natural host organisms to the engineeredcells. In some instances, enzymes can be secreted into the medium byengineered cells to degrade the alternate substrate into a form that canmore readily be taken up by the engineered cells; in other instances, abatch of engineered cells can be grown on one preferred substrate, thenlysed to liberate hydrolytic enzymes for the alternate substrate intothe medium, while a second inoculum of the same engineered host or asecond host is added to utilize the hydrolyzate.

The starting materials for recursive sequence recombination willtypically be genes for utilization of a substrate or its transport.Examples of nutrient sources of interest include but are not limited tolactose, whey, galactose, mannitol, xylan, cellobiose, cellulose andsucrose, thus allowing cheaper production of compounds including but notlimited to ethanol, tryptophan, rhamnolipid surfactants, xanthan gum,and polyhydroxylalkanoate. For a review of such substrates as desiredtarget substances, see Cameron et al. (Appl. Biochem. Biotechnol.38:105-140 (1993)).

The recursive sequence recombination methods described above can be usedto optimize the ability of native hosts or heterologous hosts to utilizea substrate of interest, to evolve more efficient transport systems, toincrease or alter specificity for certain substrates, and so on.

V. Biosynthesis

Metabolic engineering can be used to alter organisms to optimize theproduction of practically any metabolic intermediate, includingantibiotics, vitamins, amino acids such as phenylalanine and aromaticamino acids, ethanol, butanol, polymers such as xanthan gum andbacterial cellulose, peptides, and lipids. When such compounds arealready produced by a host, the recursive sequence recombinationtechniques described above can be used to optimize production of thedesired metabolic intermediate, including such features as increasingenzyme substrate specificity and turnover number, altering metabolicfluxes to reduce the concentrations of toxic substrates orintermediates, increasing resistance of the host to such toxiccompounds, eliminating, reducing or altering the need for inducers ofgene expression/activity, increasing the production of enzymes necessaryfor metabolism, etc.

Enzymes can also be evolved for improved activity in solvents other thanwater. This is useful because intermediates in chemical syntheses areoften protected by blocking groups which dramatically affect thesolubility of the compound in aqueous solvents. Many compounds can beproduced by a combination of pure chemical and enzymically catalyzedreactions. Performing enzymic reactions on almost insoluble substratesis clearly very inefficient, so the availability of enzymes that areactive in other solvents will be of great use. One example of such ascheme is the evolution of a para-nitrobenzyl esterase to removeprotecting groups from an intermediate in loracarbef synthesis (Moore,J. C. and Arnold, F. H. Nature Biotechnology 14:458-467 (1996)). In thiscase alternating rounds of error-prone PCR and colony screening forproduction of a fluorescent reporter from a substrate analogue were usedto generate a mutant esterase that was 16-fold more active than theparent molecule in 30% dimethylformamide. No individual mutation wasfound to contribute more than a 2-fold increase in activity, but it wasthe combination of a number of mutations which led to the overallincrease. Structural analysis of the mutant protein showed that theamino acid changes were distributed throughout the length of the proteinin a manner that could not have been rationally predicted. Sequentialrounds of error-prone PCR have the problem that after each round all butone mutant is discarded, with a concomitant loss of informationcontained in all the other beneficial mutations. Recursive sequencerecombination avoids this problem, and would thus be ideally suited toevolving enzymes for catalysis in other solvents, as well as inconditions where salt concentrations or pH were different from theoriginal enzyme optimas.

In addition, the yield of almost any metabolic pathway can be increased,whether consisting entirely of genes endogenous to the host organisms orall or partly heterologous genes. Optimization of the expression levelsof the enzymes in a pathway is more complex than simply maximizingexpression. In some cases regulation, rather than constitutiveexpression of an enzyme may be advantageous for cell growth andtherefore for product yield, as seen for production of phenylalanine(Backman et al. Ann. NY Acad. Sci. 589:16-24 (1990)) and2-keto-L-gluconic acid (Anderson et al. U.S. Pat. No. 5,032,514). Inaddition, it is often advantageous for industrial purposes to expressproteins in organisms other than their original hosts. New host strainsmay be preferable for a variety of reasons, including ease of cloningand transformation, pathogenicity, ability to survive in particularenvironments and a knowledge of the physiology and genetics of theorganisms. However, proteins expressed in heterologous organisms oftenshow markedly reduced activity for a variety of reasons includinginability to fold properly in the new host (Sarthy et al. Appl. Environ.Micro. 53:1996-2000 (1987)). Such difficulties can indeed be overcome bythe recursive sequence recombination strategies of the instantinvention.

A. Antibiotics

The range of natural small molecule antibiotics includes but is notlimited to peptides, peptidolactones, thiopeptides, beta-lactams,glycopeptides, lantibiotics, microcins, polyketide-derived antibiotics(anthracyclins, tetracyclins, macrolides, avermectins, polyethers andansamycins), chloramphenicol, aminoglycosides, aminocyclitols,polyoxins, agrocins and isoprenoids.

There are at least three ways in which recursive sequence recombinationtechniques of the instant invention can be used to facilitate novel drugsynthesis, or to improve biosynthesis of existing antibiotics.

First, antibiotic synthesis enzymes can be “evolved” together withtransport systems that allow entry of compounds used as antibioticprecursors to improve uptake and incorporation of function-alteringartificial side chain precursors. For example, penicillin V is producedby feeding Penicillium the artificial side chain precursor phenoxyaceticacid, and LY146032 by feeding Streptomyces roseosporus decanoic acid(Hopwood, Phil. Trans. R. Soc. Lond. B 324:549-562 (1989)). Poorprecursor uptake and poor incorporation by the synthesizing enzyme oftenlead to inefficient formation of the desired product. Recursive sequencerecombination of these two systems can increase the yield of desiredproduct.

Furthermore, a combinatorial approach can be taken in which an enzyme isshuffled for novel catalytic activity/substrate recognition (perhaps byincluding randomizing oligonucleotides in key positions such as theactive site). A number of different substrates (for example, analoguesof side chains that are normally incorporated into the antibiotic) canthen be tested in combination with all the different enzymes and testedfor biological activity. In this embodiment, plates are made containingdifferent potential antibiotic precursors (such as the side chainanalogues). The microorganisms containing the shuffled library (thelibrary strain) are replicated onto those plates, together with acompeting, antibiotic sensitive, microorganism (the indicator strain).Library cells that are able to incorporate the new side chain to producean effective antibiotic will thus be able to compete with the indicatorstrain, and will be selected for.

Second, the expression of heterologous genes transferred from oneantibiotic synthesizing organism to another can be optimized. The newlyintroduced enzyme(s) act on secondary metabolites in the host cell,transforming them into new compounds with novel properties. Usingtraditional methods, introduction of foreign genes into antibioticsynthesizing hosts has already resulted in the production of novelhybrid antibiotics. Examples include mederrhodin, dihydrogranatirhodin,6-deoxyerythromycin A, isovalerylspiramycin and other hybrid macrolides(Cameron et. al. Appl. Biochem. Biotechnol. 38:105-140 (1993)). Therecursive sequence recombination techniques of the instant invention canbe used to optimize expression of the foreign genes, to stabilize theenzyme in the new host cell, and to increase the activity of theintroduced enzyme against its new substrates in the new host cell. Insome embodiments of the invention, the host genome may also be sooptimized.

Third, the substrate specificity of an enzyme involved in secondarymetabolism can be altered so that it will act on and modify a newcompound or so that its activity is changed and it acts at a differentsubset of positions of its normal substrate. Recursive sequencerecombination can be used to alter the substrate specificities ofenzymes. Furthermore, in addition to recursive sequence recombination ofindividual enzymes being a strategy to generate novel antibiotics,recursive sequence recombination of entire pathways, by altering enzymeratios, will alter metabolite fluxes and may result, not only inincreased antibiotic synthesis, but also in the synthesis of differentantibiotics. This can be deduced from the observation that expression ofdifferent genes from the same cluster in a foreign host leads todifferent products being formed (see p. 80 in Hutchinson et. al., (1991)Ann NY Acad Sci, 646:78-93). Recursive sequence recombination of theintroduced gene clusters may result in a variety of expression levels ofdifferent proteins within the cluster (because it produces differentcombinations of, in this case regulatory, mutations). This in turn maylead to a variety of different end products. Thus, “evolution” of anexisting antibiotic synthesizing pathway could be used to generate novelantibiotics either by modifying the rates or substrate specificities ofenzymes in that pathway.

Additionally, antibiotics can also be produced in vitro by the action ofa purified enzyme on a precursor. For example isopenicillin N synthasecatalyses the cyclization of many analogues of its normal substrate(d-(L-a-aminoadipyl)-L-cysteinyl-D-valine) (Hutchinson, Med. Res. Rev.8:557-567 (1988)). Many of these products are active as antibiotics. Awide variety of substrate analogues can be tested for incorporation bysecondary metabolite synthesizing enzymes without concern for theinitial efficiency of the reaction. Recursive sequence recombination canbe used subsequently to increase the rate of reaction with a promisingnew substrate.

Thus, organisms already producing a desired antibiotic can be evolvedwith the recursive sequence recombination techniques described above tomaximize production of that antibiotic. Additionally, new antibioticscan be evolved by manipulation of genetic material from the host by therecursive sequence recombination techniques described above. Genes forantibiotic production can be transferred to a preferred host aftercycles of recursive sequence recombination or can be evolved in thepreferred host as described above. Antibiotic genes are generallyclustered and are often positively regulated, making them especiallyattractive candidates for the recursive sequence recombinationtechniques of the instant invention. Additionally, some genes of relatedpathways show cross-hybridization, making them preferred candidates forthe generation of new pathways for new antibiotics by the recursivesequence recombination techniques of the invention. Furthermore,increases in secondary metabolite production including enhancement ofsubstrate fluxes (by increasing the rate of a rate limiting enzyme,deregulation of the pathway by suppression of negative control elementsor over expression of activators and the relief of feedback controls bymutation of the regulated enzyme to a feedback-insensitive deregulatedprotein) can be achieved by recursive sequence recombination withoutexhaustive analysis of the regulatory mechanisms governing expression ofthe relevant gene clusters.

The host chosen for expression of evolved genes is preferably resistantto the antibiotic produced, although in some instances productionmethods can be designed so as to sacrifice host cells when the amount ofantibiotic produced is commercially significant yet lethal to the host.Similarly, bioreactors can be designed so that the growth medium iscontinually replenished, thereby “drawing off” antibiotic produced andsparing the lives of the producing cells. Preferably, the mechanism ofresistance is not the degradation of the antibiotic produced.

Numerous screening methods for increased antibiotic expression are knownin the art, as discussed above, including screening for organisms thatare more resistant to the antibiotic that they produce. This may resultfrom linkage between expression of the antibiotic synthesis andantibiotic resistance genes (Chater, Bio/Technology 8:115-121 (1990)).Another screening method is to fuse a reporter gene (e.g. xylE from thePseudomonas TOL plasmid) to the antibiotic production genes. Antibioticsynthesis gene expression can then be measured by looking for expressionof the reporter (e.g. xylE encodes a catechol dioxygenase which producesyellow muconic semialdehyde when colonies are sprayed with catechol(Zukowski et al. Proc. Natl. Acad. Sci. U.S.A. 80:1101-1105 (1983)).

The wide variety of cloned antibiotic genes provides a wealth ofstarting materials for the recursive sequence recombination techniquesof the instant invention. For example, genes have been cloned fromStreptomyces cattleya which direct cephamycin C synthesis in thenon-antibiotic producer Streptomyces lividans (Chen et al.Bio/Technology 6:1222-1224 (1988)). Clustered genes for penicillinbiosynthesis (δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine synthetase;isopenicillin N synthetase and acyl coenzyme A:6-aminopenicillanic acidacyltransferase) have been cloned from Penicillium chrysogenum. Transferof these genes into Neurospora crassa and Aspergillus niger result inthe synthesis of active penicillin V (Smith et al. Bio/Technology8:39-41 (1990)). For a review of cloned genes involved in CephalosporinC, Penicillins G and V and Cephamycin C biosynthesis, see Piepersberg,Crit. Rev. Biotechnol. 14:251-285 (1994). For a review of clonedclusters of antibiotic-producing genes, see Chater Bio/Technolooy8:115-121 (1990). Other examples of antibiotic synthesis genestransferred to industrial producing strains, or over expression ofgenes, include tylosin, cephamycin C, cephalosporin C, LL-E33288 complex(an antitumor and antibacterial agent), doxorubicin, spiramycin andother macrolide antibiotics, reviewed in Cameron et al. Appl. Biochem.Biotechnol. 38:105-140 (1993).

B. Biosynthesis to Replace Chemical Synthesis of Antibiotics

Some antibiotics are currently made by chemical modifications ofbiologically produced starting compounds. Complete biosynthesis of thedesired molecules may currently be impractical because of the lack of anenzyme with the required enzymatic activity and substrate specificity.For example, 7-aminodeacetooxycephalosporanic acid (7-ADCA) is aprecursor for semi-synthetically produced cephalosporins. 7-ADCA is madeby a chemical ring expansion from penicillin V followed by enzymaticdeacylation of the phenoxyacetal group. Cephalosporin V could inprinciple be produced biologically from penicillin V using penicillin Nexpandase, but penicillin V is not used as a substrate by any knownexpandase. The recursive sequence recombination techniques of theinvention can be used to alter the enzyme so that it will use penicillinV as a substrate. Similarly, penicillin transacylase could be somodified to accept cephalosporins or cephamycins as substrates.

In yet another example, penicillin amidase expressed in E. coli is a keyenzyme in the production of penicillin G derivatives. The enzyme isgenerated from a precursor peptide and tends to accumulate as insolubleaggregates in the periplasm unless non-metabolizable sugars are presentin the medium (Scherrer et al. Appl. Microbiol. Biotechnol. 42:85-91(1994)). Evolution of this enzyme through the methods of the instantinvention could be used to generate an enzyme that folds better, leadingto a higher level of active enzyme expression.

In yet another example, Penicillin G acylase covalently linked toagarose is used in the synthesis of penicillin G derivatives. The enzymecan be stabilized for increased activity, longevity and/or thermalstability by chemical modification (Fernandez-Lafuente et. al. EnzymeMicrob. Technol. 14:489-495 (1992). Increased thermal stability is anespecially attractive application of the recursive sequencerecombination techniques of the instant invention, which can obviate theneed for the chemical modification of such enzymes. Selection forthermostability can be performed in vivo in E. coli or in thermophilesat higher temperatures. In general, thermostability is a good first stepin enhancing general stabilization of enzymes. Random mutagenesis andselection can also be used to adapt enzymes to function in non-aqueoussolvents (Arnold Curr Opin Biotechnol, 4:450-455 (1993); Chen et. al.Proc. Natl. Acad. Sci. U.S.A., 90:5618-5622 (1993)). Recursive sequencerecombination represents a more powerful (since recombinogenic) methodof generating mutant enzymes that are stable and active in non-aqueousenvironments. Additional screening can be done on the basis of enzymestability in solvents.

C. Polyketides

Polyketides include antibiotics such as tetracycline and erythromycin,anti-cancer agents such as daunomycin, immunosuppressants such as FK506and rapamycin and veterinary products such as monesin and avermectin.Polyketide synthases (PKS's) are multifunctional enzymes that controlthe chain length, choice of chain-building units and reductive cyclethat generates the huge variation in naturally occurring polyketides.Polyketides are built up by sequential transfers of “extender units”(fatty acyl CoA groups) onto the appropriate starter unit (examples areacetate, coumarate, propionate and malonamide). The PKS's determine thenumber of condensation reactions and the type of extender groups addedand may also fold and cyclize the polyketide precursor. PKS's reducespecific β-keto groups and may dehydrate the resultant β-hydroxyls toform double bonds. Modifications of the nature or number of buildingblocks used, positions at which β-keto groups are reduced, the extent ofreduction and different positions of possible cyclizations, result information of different final products. Polyketide research is currentlyfocused on modification and inhibitor studies, site directed mutagenesisand 3-D structure elucidation to lay the groundwork for rational changesin enzymes that will lead to new polyketide products.

Recently, McDaniel et al. (Science 262:1546-1550 (1995)) have developeda Streptomyces host-vector system for efficient construction andexpression of recombinant PKSs. Hutchinson (Bio/Technology 12:375-308(1994)) reviewed targeted mutation of specific biosynthetic genes andsuggested that microbial isolates can be screened by DNA hybridizationfor genes associated with known pharmacologically active agents so as toprovide new metabolites and large amounts of old ones. In particular,that review focuses on polyketide synthase and pathways toaminoglycoside and oligopeptide antibiotics.

The recursive sequence recombination techniques of the instant inventioncan be used to generate modified enzymes that produce novel polyketideswithout such detailed analytical effort. The availability of the PKSgenes on plasmids and the existence of E. coli-Streptomyces shuttlevectors (Wehmeier Gene 165:149-150 (1995)) makes the process ofrecursive sequence recombination especially attractive by the techniquesdescribed above. Techniques for selection of antibiotic producingorganisms can be used as described above; additionally, in someembodiments screening for a particular desired polyketide activity orcompound is preferable.

D. Isoprenoids

Isoprenoids result from cyclization of farnesyl pyrophosphate bysesquiterpene synthases. The diversity of isoprenoids is generated notby the backbone, but by control of cyclization. Cloned examples ofisoprenoid synthesis genes include trichodiene synthase from Fusariumsprorotrichioides, pentalene synthase from Streptomyces, aristolochenesynthase from Penicillium roquefortii, and epi-aristolochene synthasefrom N. tabacum (Cane, D. E. (1995). Isoprenoid antibiotics, pages633-655, in “Genetics and Biochemistry of Antibiotic Production” editedby Vining, L.C. & Stuttard, C., published by Butterworth-Heinemann).Recursive sequence recombination of sesquiterpene synthases will be ofuse both in allowing expression of these enzymes in heterologous hosts(such as plants and industrial microbial strains) and in alteration ofenzymes to change the cyclized product made. A large number ofisoprenoids are active as antiviral, antibacterial, antifungal,herbicidal, insecticidal or cytostatic agents. Antibacterial andantifungal isoprenoids could thus be preferably screened for using theindicator cell type system described above, with the producing cellcompeting with bacteria or fungi for nutrients. Antiviral isoprenoidscould be screened for preferably by their ability to confer resistanceto viral attack on the producing cell.

E. Bioactive Peptide Derivatives

Examples of bioactive non-ribosomally synthesized peptides include theantibiotics cyclosporin, pepstatin, actinomycin, gramicidin,depsipeptides, vancomycin, etc. These peptide derivatives aresynthesized by complex enzymes rather than ribosomes. Again, increasingthe yield of such non-ribosomally synthesized peptide antibiotics hasthus far been done by genetic identification of biosynthetic“bottlenecks” and over expression of specific enzymes (See, for example,p. 133-135 in “Genetics and Biochemistry of Antibiotic Production”edited by Vining, L.C. & Stuttard, C., published byButterworth-Heinemann). Recursive sequence recombination of the enzymeclusters can be used to improve the yields of existing bioactivenon-ribosomally made peptides in both natural and heterologous hosts.Like polyketide synthases, peptide synthases are modular andmultifunctional enzymes catalyzing condensation reactions betweenactivated building blocks (in this case amino acids) followed bymodifications of those building blocks (see Kleinkauf, H. and vonDohren, H. Eur. J. Biochem. 236:335-351 (1996)). Thus, as for polyketidesynthases, recursive sequence recombination can also be used to alterpeptide synthases: modifying the specificity of the amino acidrecognized by each binding site on the enzyme and altering the activityor substrate specificities of sites that modify these amino acids toproduce novel compounds with antibiotic activity.

Other peptide antibiotics are made ribosomally and thenpost-translationally modified. Examples of this type of antibiotics arelantibiotics (produced by gram positive bacteria such Staphylococcus,Streptomyces, Bacillus, and Actinoplanes) and microcins (produced byEnterobacteriaceae). Modifications of the original peptide include (inlantibiotics) dehydration of serine and threonine, condensation ofdehydroamino acids with cysteine, or simple N- and C-terminal blocking(microcins). For ribosomally made antibiotics both the peptide-encodingsequence and the modifying enzymes may have their expression levelsmodified by recursive sequence recombination. Again, this will lead toboth increased levels of antibiotic synthesis, and by modulation of thelevels of the modifying enzymes (and the sequence of the ribosomallysynthesized peptide itself) novel antibiotics.

Screening can be done as for other antibiotics as described above,including competition with a sensitive (or even initially insensitive)microbial species. Use of competing bacteria that have resistances tothe antibiotic being produced will select strongly either for greatlyelevated levels of that antibiotic (so that it swamps out the resistancemechanism) or for novel derivatives of that antibiotic that are notneutralized by the resistance mechanism.

F. Polymers

Several examples of metabolic engineering to produce biopolymers havebeen reported, including the production of the biodegradable plasticpolyhydroxybutarate (PHB), and the polysaccharide xanthan gum. For areview, see Cameron et al. Applied Biochem. Biotech. 38:105-140 (1993).Genes for these pathways have been cloned, making them excellentcandidates for the recursive sequence recombination techniques describedabove. Expression of such evolved genes in a commercially viable hostsuch as E. coli is an especially attractive application of thistechnology.

Examples of starting materials for recursive sequence recombinationinclude but are not limited to genes from bacteria such as Alcaligenes,Zoogloea, Rhizobium, Bacillus, and Azobacter, which producepolyhydroxyalkanoates (PHAs) such as polyhyroxybutyrate (PHB)intracellularly as energy reserve materials in response to stress. Genesfrom Alcaligenes eutrophus that encode enzymes catalyzing the conversionof acetoacetyl CoA to PHB have been transferred both to E. coli and tothe plant Arabidopsis thaliana (Poirier et al. Science 256:520-523(1992)). Two of these genes (phbB and phbc, encoding acetoacetyl-CoAreductase and PHB synthase respectively) allow production of PHB inArabidopsis. The plants producing the plastic are stunted, probablybecause of adverse interactions between the new metabolic pathway andthe plants' original metabolism (i.e., depletion of substrate from themevalonate pathway). Improved production of PHB in plants has beenattempted by localization of the pathway enzymes to organelles such asplastids. Other strategies such as regulation of tissue specificity,expression timing and cellular localization have been suggested to solvethe deleterious effects of PHB expression in plants. The recursivesequence recombination techniques of the invention can be used to modifysuch heterologous genes as well as specific cloned interacting pathways(e.g., mevalonate), and to optimize PHB synthesis in industrialmicrobial strains, for example to remove the requirement for stresses(such as nitrogen limitation) in growth conditions.

Additionally, other microbial polyesters are made by different bacteriain which additional monomers are incorporated into the polymer (Peopleset al. in Novel Biodegradable Microbial Polymers, E A Dawes, ed.,pp191-202 (1990)). Recursive sequence recombination of these genes orpathways singly or in combination into a heterologous host will allowthe production of a variety of polymers with differing properties,including variation of the monomer subunit ratios in the polymer.Another polymer whose synthesis may be manipulated by recursive sequencerecombination is cellulose. The genes for cellulose biosynthesis havebeen cloned from Agrobacterium tumefaciens (Matthysse, A. G. et. al. J.Bacteriol. 177:1069-1075 (1995)). Recursive sequence recombination ofthis biosynthetic pathway could be used either to increase synthesis ofcellulose, or to produce mutants in which alternative sugars areincorporated into the polymer.

G. Carotenoids

Carotenoids are a family of over 600 terpenoids produced in the generalisoprenoid biosynthetic pathway by bacteria, fungi and plants (for areview, see Armstrong, J. Bact. 176:4795-4802 (1994)). These pigmentsprotect organisms against photooxidative damage as well as functioningas anti-tumor agents, free radical-scavenging anti-oxidants, andenhancers of the immune response. Additionally, they are usedcommercially in pigmentation of cultured fish and shellfish. Examples ofcarotenoids include but are not limited to myxobacton, spheroidene,spheroidenone, lutein, astaxanthin, violaxanthin, 4-ketorulene,myxoxanthrophyll, echinenone, lycopene, zeaxanthin and its mono- and di-glucosides, α-, β-, γ- and δ-carotene, β-cryptoxanthin monoglucoside andneoxanthin.

Carotenoid synthesis is catalyzed by relatively small numbers ofclustered genes: 11 different genes within 12 kb of DNA from Myxococcusxanthus (Botella et al. Eur. J. Biochem. 233:238-248 (1995)) and 8 geneswithin 9 kb of DNA from Rhodobacter sphaeroides (Lang et. al. J. Bact.177:2064-2073 (1995)). In some microorganisms, such as Thermusthermophilus, these genes are plasmid-borne (Tabata et al. FEBS Letts341:251-255 (1994)). These features make carotenoid synthetic pathwaysespecially attractive candidates for recursive sequence recombination.

Transfer of some carotenoid genes into heterologous organisms results inexpression. For example, genes from Erwina uredovora and Haematococcuspluvialis will function together in E. coli (Kajiwara et al. Plant Mol.Biol. 29:343-352 (1995)). E. herbicola genes will function in R.sphaeroides (Hunter et al. J. Bact. 176:3692-3697 (1994)). However, someother genes do not; for example, R. capsulatus genes do not directcarotenoid synthesis in E. coli (Marrs, J. Bact. 146:1003-1012 (1981)).

In an embodiment of the invention, the recursive sequence recombinationtechniques of the invention can be used to generate variants in theregulatory and/or structural elements of genes in the carotenoidsynthesis pathway, allowing increased expression in heterologous hosts.Indeed, traditional techniques have been used to increase carotenoidproduction by increasing expression of a rate limiting enzyme in Thermusthermophilus (Hoshino et al. Appl. Environ. Micro. 59:3150-3153 (1993)).Furthermore, mutation of regulatory genes can cause constitutiveexpression of carotenoid synthesis in actinomycetes, where carotenoidphotoinducibility is otherwise unstable and lost at a relatively highfrequency in some species (Kato et al. Mol. Gen. Genet. 247:387-390(1995)). These are both mutations that can be obtained by recursivesequence recombination.

The recursive sequence recombination techniques of the invention asdescribed above can be used to evolve one or more carotenoid synthesisgenes in a desired host without the need for analysis of regulatorymechanisms. Since carotenoids are colored, a calorimetric assay inmicrotiter plates, or even on growth media plates, can be used forscreening for increased production.

In addition to increasing expression of carotenoids, carotenogenicbiosynthetic pathways have the potential to produce a wide diversity ofcarotenoids, as the enzymes involved appear to be specific for the typeof reaction they will catalyze, but not for the substrate that theymodify. For example, two enzymes from the marine bacterium Agrobacteriumaurantiacum (CrtW and CrtZ) synthesize six different ketocarotenoidsfrom β-carotene (Misawa et al. J. Bact. 177:6576-6584 (1995)). Thisrelaxed substrate specificity means that a diversity of substrates canbe transformed into an even greater diversity of products. Introductionof foreign carotenoid genes into a cell can lead to novel and functionalcarotenoid-protein complexes, for example in photosynthetic complexes(Hunter et al. J. Bact. 176:3692-3697 (1994)). Thus, the deliberaterecombination of enzymes through the recursive sequence recombinationtechniques of the invention is likely to generate novel compounds.Screening for such compounds can be accomplished, for example, by thecell competition/survival techniques discussed above and by acalorimetric assay for pigmented compounds.

Another method of identifying new compounds is to use standardanalytical techniques such as mass spectroscopy, nuclear magneticresonance, high performance liquid chromatography, etc. Recombinantmicroorganisms can be pooled and extracts or media supernatants assayedfrom these pools. Any positive pool can then be subdivided and theprocedure repeated until the single positive is identified(“sib-selection”).

H. Indigo Biosynthesis

Many dyes, i.e. agents for imparting color, are specialty chemicals withsignificant markets. As an example, indigo is currently producedchemically. However, nine genes have been combined in E. coli to allowthe synthesis of indigo from glucose via the tryptophan/indole pathway(Murdock et al. Bio/Technology 11:381-386 (1993)). A number ofmanipulations were performed to optimize indigo synthesis: cloning ofnine genes, modification of the fermentation medium and directed changesin two operons to increase reaction rates and catalytic activities ofseveral enzymes. Nevertheless, bacterially produced indigo is notcurrently an economic proposition. The recursive sequence recombinationtechniques of the instant invention could be used to optimize indigosynthesizing enzyme expression levels and catalytic activities, leadingto increased indigo production, thereby making the process commerciallyviable and reducing the environmental impact of indigo manufacture.Screening for increased indigo production can be done by colorimetricassays of cultures in microtiter plates.

I. Amino Acids

Amino acids of particular commercial importance include but are notlimited to phenylalanine, monosodium glutamate, glycine, lysine,threonine, tryptophan and methionine. Backman et al. (Ann. NY Acad. Sci.589:16-24 (1990)) disclosed the enhanced production of phenylalanine inE. coli via a systematic and downstream strategy covering organismselection, optimization of biosynthetic capacity, and development offermentation and recovery processes.

As described in Simpson et al. (Biochem Soc Trans, 23:381-387 (1995)),current work in the field of amino acid production is focused onunderstanding the regulation of these pathways in great moleculardetail. The recursive sequence recombination techniques of the instantinvention would obviate the need for this analysis to obtain bacterialstrains with higher secreted amino acid yields. Amino acid productioncould be optimized for expression using recursive sequence recombinationof the amino acid synthesis and secretion genes as well as enzymes atthe regulatory phosphoenolpyruvate branchpoint, from such organisms asSerratia marcescens, Bacillus, and the Corynebacterium-Brevibacteriumgroup. In some embodiments of the invention, screening for enhancedproduction is preferably done in microtiter wells, using chemical testswell known in the art that are specific for the desired amino acid.Screening/selection for amino acid synthesis can also be done by usingauxotrophic reporter cells that are themselves unable to synthesize theamino acid in question. If these reporter cells also produce a compoundthat stimulates the growth of the amino acid producer (this could be agrowth factor, or even a different amino acid), then library cells thatproduce more amino acid will in turn receive more growth stimulant andwill therefore grow more rapidly.

J. Vitamin C synthesis

L-Ascorbic acid (vitamin C) is a commercially important vitamin with aworld production of over 35,000 tons in 1984. Most vitamin C iscurrently manufactured chemically by the Reichstein process, althoughrecently bacteria have been engineered that are able to transformglucose to 2,5-keto-gluconic acid, and that product to 2-keto-L-idonicacid, the precursor to L-ascorbic acid (Boudrant, Enzyme Microb.Technol. 12:322-329 (1990)).

The efficiencies of these enzymatic steps in bacteria are currently low.Using the recursive sequence recombination techniques of the instantinvention, the genes can be genetically engineered to create one or moreoperons followed by expression optimization of such a hybrid L-ascorbicacid synthetic pathway to result in commercially viable microbialvitamin C biosynthesis. In some embodiments, screening for enhancedL-ascorbic acid production is preferably done in microtiter plates,using assays well known in the art.

VI. Modification of Cell Properties.

Although not strictly examples of manipulation of intermediarymetabolism, recursive sequence recombination techniques can be used toimprove or alter other aspects of cell properties, from growth rate toability to secrete certain desired compounds to ability to tolerateincreased temperature or other environmental stresses. Some examples oftraits engineered by traditional methods include expression ofheterologous proteins in bacteria, yeast, and other eukaryotic cells,antibiotic resistance, and phage resistance. Any of these traits isadvantageously evolved by the recursive sequence recombinationtechniques of the instant invention. Examples include replacement of onenutrient uptake system (e.g. ammonia in Methylophilus methylotrophus)with another that is more energy efficient; expression of haemoglobin toimprove growth under conditions of limiting oxygen; redirection of toxicmetabolic end products to less toxic compounds; expression of genesconferring tolerance to salt, drought and toxic compounds and resistanceto pathogens, antibiotics and bacteriophage, reviewed in Cameron et. al.Appl Biochem Biotechnol, 38:105-140 (1993).

The heterologous genes encoding these functions all have the potentialfor further optimization in their new hosts by existing recursivesequence recombination technology. Since these functions increase cellgrowth rates under the desired growth conditions, optimization of thegenes by evolution simply involves recombining the DNA recursively andselecting the recombinants that grow faster with limiting oxygen, highertoxic compound concentration, or whatever is the appropriate growthcondition for the parameter being improved.

Since these functions increase cell growth rates under the desiredgrowth conditions, optimization of the genes by “evolution” can simplyinvolve “shuffling” the DNA and selecting the recombinants that growfaster with limiting oxygen, higher toxic compound concentration orwhatever restrictive condition is being overcome.

Cultured mammalian cells also require essential amino acids to bepresent in the growth medium. This requirement could also becircumvented by expression of heterologous metabolic pathways thatsynthesize these amino acids (Rees et al. Biotechnology 8:629-633(1990). Recursive sequence recombination would provide a mechanism foroptimizing the expression of these genes in mammalian cells. Once again,a preferred selection would be for cells that can grow in the absence ofadded amino acids.

Yet another candidate for improvement through the techniques of theinvention is symbiotic nitrogen fixation. Genes involved in nodulation(nod, ndv), nitrogen reduction (nif, fix), host range determination(nod, hsp), bacteriocin production (tfx), surface polysaccharidesynthesis (exo) and energy utilization (dct, hup) which have beenidentified (Paau, Biotech. Adv. 9:173-184 (1991)).

The main function of recursive sequence recombination in this case is inimproving the survival of strains that are already known to be betternitrogen fixers. These strains tend to be less good at competing withstrains already present in the environment, even though they are betterat nitrogen fixation. Targets for recursive sequence recombination suchas nodulation and host range determination genes can be modified andselected for by their ability to grow on the new host. Similarly anybacteriocin or energy utilization genes that will improve thecompetitiveness of the strain will also result in greater growth rates.Selection can simply be performed by subjecting the target genes torecursive sequence recombination and forcing the inoculant to competewith wild type nitrogen fixing bacteria. The better the nitrogen fixingbacteria grow in the new host, the more copies of their recombined geneswill be present for the next round of recombination. This growth ratedifferentiating selection is described above in detail.

VI. Biodetectors/Biosensors

Bioluminescence or fluorescence genes can be used as reporters by fusingthem to specific regulatory genes (Cameron et. al. Appl BiochemBiotechnol, 38:105-140 (1993)). A specific example is one in which theluciferase genes luxCDABE of Vibrio fischeri were fused to theregulatory region of the isopropylbenzene catabolism operon fromPseudomonas putida RE204. Transformation of this fusion construct intoE. coli resulted in a strain which produced light in response to avariety of hydrophobic compound such as substituted benzenes,chlorinated solvents and naphthalene (Selifonova et. al., Appl EnvironMicrobiol 62:778-783 (1996)). This type of construct is useful for thedetection of pollutant levels, and has the added benefit of onlymeasuring those pollutants that are bioavailable (and thereforepotentially toxic). Other signal molecules such as jellyfish greenfluorescent protein could also be fused to genetic regulatory regionsthat respond to chemicals in the environment. This should allow avariety of molecules to be detected by their ability to induceexpression of a protein or proteins which result in light, fluorescenceor some other easily detected signal.

Recursive sequence recombination can be used in several ways to modifythis type of biodetection system. It can be used to increase theamplitude of the response, for example by increasing the fluorescence ofthe green fluorescent protein. Recursive sequence recombination couldalso be used to increase induced expression levels or catalyticactivities of other signal-generating systems, for example of theluciferase genes.

Recursive sequence recombination can also be used to alter thespecificity of biosensors. The regulatory region, and transcriptionalactivators that interact with this region and with the chemicals thatinduce transcription can also be shuffled. This should generateregulatory systems in which transcription is activated by analogues-ofthe normal inducer, so that biodetectors for different chemicals can bedeveloped. In this case, selection would be for constructs that areactivated by the (new) specific chemical to be detected. Screening couldbe done simply with fluorescence (or light) activated cell sorting,since the desired improvement is in light production.

In addition to detection of environmental pollutants, biosensors can bedeveloped that will respond to any chemical for which there arereceptors, or for which receptors can be evolved by recursive sequencerecombination, such as hormones, growth factors, metals and drugs. Thesereceptors may be intracellular and direct activators of transcription,or they may be membrane bound receptors that activate transcription ofthe signal indirectly, for example by a phosphorylation cascade. Theymay also not act on transcription at all, but may produce a signal bysome post-transcriptional modification of a component of the signalgenerating pathway. These receptors may also be generated by fusingdomains responsible for binding different ligands with differentsignaling domains. Again, recursive sequence recombination can be usedto increase the amplitude of the signal generated to optimize expressionand functioning of chimeric receptors, and to alter the specificity ofthe chemicals detected by the receptor.

The following examples are offered by way of illustration, not by way oflimitation.

EXAMPLES

I. Alteration of enzyme activity and specificity.

In this example, recursive sequence recombination techniques of theinstant invention were used to expand the range of substratesefficiently hydrolyzed by E. coli β-galactosidase. The goal was toevolve wild type E. coli β-galactosidase into a fucosidase. The enzymeshowed very weak activity with both ρ-nitrophenyl-β-D-fucopyranoside ando-nitrophenyl-β-D-fucopyranoside (estimated respectively as 80- and160-fold less efficient than for ρ-nitrophenyl-β-D-galactopyranoside).

To increase the activity of E. coli β-galactosidase against thesefucopyranoside derivatives, a lacZ gene (a 3.8 kb Hind III -BamHIfragment from plasmid pCH110, Pharmacia) encoding E. coliβ-galactosidase was subcloned into plasmid p18SFI-BLA-SFI (Stemmer,Nature, 370:389-391 (1994)). The resulting plasmid, p18-lacZ, was usedfor recursive sequence recombination and mutant screening.

Purified plasmid pl8-lacZ (4-5 μg) was used directly for DNase Ifragmentation. Fragments with sizes between 50 and 200 bp were purifiedfrom a 2% agarose gel and used for reassembly PCR (Stemmer, Nature370:389-391 (1994)). Assembly reactions used Tth polymerase (PerkinElmer) in the manufacturer's supplied buffer. The PCR program forassembly was as follows: 94° C., 2 min., then 40 cycles of 94° C. for 30sec.; 55° C. for 3 sec.; 72° C. for 1 min.+5 sec. per cycle; thenfinally 72° C. for 5 min.

This reaction was diluted 100-fold into a standard PCR reaction usingthe 40mer primers p50F5′-AGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCC-3′(SEQ ID NO:1) and pR345′-CTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCAT-3′(SEQ ID NO:2). Thisresulted in amplification of both the desired DNA band (about 4 kb insize) as well as two smaller sized products (about 600 bp and 100 bpbands). The PCR products were digested with BamHI and Hind III and thecorrect size product was cloned into BamHI-HindIII digested p18-lacZ.The resulting plasmid containing a pool of recombined lacZ mutants wasplated out on LB plates supplemented with kanamycin and5-bromo-4-chloro-3-indolyl-β-D-fucopyranoside (X-fuco). Plates wereincubated at 37° C. for 20 hours and screened for colonies with slightblue tint, indicating hydrolysis of the X-fuco. Plasmid DNA was preparedfrom positive colonies and the procedure was repeated. Thus, six roundsof recursive sequence recombination produced a ten-fold increase inX-fuco hydrolysis activity.

II. Evolution of an Entire Metabolic Pathway

As an example of evolution of an entire metabolic pathway, the recursivesequence recombination techniques of the invention were used to modify aplasmid encoding resistance to mercury salts. This plasmid, as disclosedby Wang et al. (J. Bact. 171:83-92 (1989)) contains at least 8 geneswithin 13.5 kb of Bacillus DNA inserted in the cloning vector pUC9. Therecursive sequence recombination protocol used for this plasmid was asfollows.

Plasmid DNA (at 130 Ag/ml) was digested with 0.09 U/ml DNAse in 50 mMTris-Cl, pH 7.4, 10 mM MnCl₂, for 10 minutes at 25° C. DNA fragmentswere not size-selected, but were purified by phenol extraction andethanol precipitation. The assembly reaction was performed using Tthpolymerase (Perkin Elmer) using the manufacturer's supplied buffer,supplemented with the following: 7.5% polyethylene glycol, 8000 MW; 35mM tetramethylammonium chloride; and 4 U/ml Pwo(Boehringer Mannheim),Pfu(Stratagene), Vent (New England Biolabs), Deep Vent (New EnglandBiolabs), Tfl (Promega) or Tli (Promega) thermostable DNA polymerases.DNA fragments were used at around 10 μg/ml.

The PCR program for assembly was as follows: 94° C. for 20 sec., then 40cycles of 94° C. for 15 sec., 40° C. for 30 sec., 72° C. for 30 sec.+2sec./cycle, and finally 72° C. for 10 min.

The recombinant plasmid was then amplified in three fragments by usingprimers flanking the three relatively evenly spaced AlwNI restrictionsites contained in the plasmid. The sequences of these primers were:

1) 5′-CAGGACTTATCGCCACTGGCAGC-3′(SEQ ID NO:3)

2) 5′-CTCGCTCTGCTAATCCTGTTACC-3′(SEQ ID NO:4)

3) 5′-GCATATTATGAGCGTTTAGGCTTAATTCC-3′(SEQ ID NO:5)

4) 5′-CGGTATCCTTTTTCCGTACGTTC-3′(SEQ ID NO:6)

5) 5′-GTTGAAGAGGTGAAGAAAGTTCTCC-3′(SEQ ID NO:7)

6) 5′-GTTCGTCGATTTCCACGCTTGGC-3′(SEQ ID NO:8).

Three fragments were amplified using primers 1+4 (6 kb fragment), 2+5 (4kb fragment) and 3+6 (6 kb fragment). These were then digested withAlwNI, gel purified and ligated together. As AlwNI is a non-palindromiccutter, the plasmid could only reassemble in the correct (original)order. The resultant plasmids were transformed into E. coli strain DH1OB(Gibco BRL) and selected on nutrient agar containing ampicillin 50 μ/mland increasing concentrations of mercuric chloride (100 μM to 1000 μM)or phenylmercuric acetate (50 μM to 400 μM) Thus, in 2 rounds ofrecursive sequence recombination the tolerance of E. coli to thesecompounds increased by a factor of 10 (from about 100 to about 1,000μM).

III. Recursive sequence Recombination of a Family of Related Enzymes

In this example nucleotide sequences were recombined between fourhomologous β-lactamases from C. freundii, E. cloacae, K. pneumonia, andY. enterocolitica. The four genes were synthesized from oligonucleotidesas described in Stemmer, et al. Gene 164:49-53 (1995). Briefly, theentire coding sequences of the genes were synthesized as overlapping50-mer oligonucleotides on a commercial oligonucleotide synthesizer. Theoligonucleotides were then assembled into full length genes by astandard recursive sequence recombination reaction, followed byamplification using primers common to all four genes. oligonucleotideswere designed to give optimal E. coli codon usage in the synthetic geneswith the goal of increasing the homology to increase the frequency ofrecombination, and the same 5′ and 3′ terminal sequences. After assemblyof the genes and selection for active clones, which is optional, theywere DNase treated to produce fragments from 50 to 200 bp in length. Thefragments were dissolved at 100 μg/ml in 15 μl of Klenow (DNA polymeraseI large fragment) buffer (New England Biolabs) and subjected to manualPCR as follows: 15 cycles of 95° C. for 1 min.; freeze on dry ice andethanol; warm to 25° C. and add 2 μl of Klenow (1 U/μl) in Klenowbuffer; incubate for 2 min at 25° C.

A 5 μl aliquot of the manual PCR reaction was then diluted 6-fold into astandard Taq reaction mix (without oligonucleotide primers) andassembled using a standard PCR program consisting of 30 cycles of 94° C.for 30 sec., 40° C. for 30 sec., and 72° C. for 30 sec.

A 4, 8 or 16 μl aliquot of this second PCR reaction was then dilutedinto a standard Taq reaction mix containing oligonucleotide primers thatprime on sequences contained in all four β-lactamase genes5′-AGGGCCTCGTGATACGCCTATT-3′(SEQ ID NO:9) and5′-ACGAAAACTCACGTTAAGGGATT-3′(SEQ ID NO:10). Full-length product wasamplified using a standard PCR program consisting of 25 cycles of 94° C.for 30 sec., 45° C. for 30 sec., 72° C. for 45 sec.

This procedure produced hybrid β-lactamase genes whose activities can betested against antibiotics including but not limited to ampicillin,carbenicillin, cefotaxime, cefoxitine, cloxacillin, ceftazidime,cephaloridine and moxalactam, to determine the specificities of thehybrid enzymes so created. Moxalactam was chosen as the test antibioticfor hybrid genes. The best of the original β-lactamase genes used inthis study conferred resistance to 0.125 μg/ml of moxalactam. After thefirst round of-recursive sequence recombination hybrid genes wereisolated that conferred resistance to 0.5 μg/ml moxalactam, yielding a4-fold increase.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims.

All references cited herein are expressly incorporated in their entiretyfor all purposes.

10 40 base pairs nucleic acid single linear DNA (genomic) 1 AGCGCCCAATACGCAAACCG CCTCTCCCCG CGCGTTGGCC 40 40 base pairs nucleic acid singlelinear DNA (genomic) 2 CTATGCGGCA TCAGAGCAGA TTGTACTGAG AGTGCACCAT 40 23base pairs nucleic acid single linear DNA (genomic) 3 CAGGACTTATCGCCACTGGC AGC 23 23 base pairs nucleic acid single linear DNA (genomic)4 CTCGCTCTGC TAATCCTGTT ACC 23 29 base pairs nucleic acid single linearDNA (genomic) 5 GCATATTATG AGCGTTTAGG CTTAATTCC 29 23 base pairs nucleicacid single linear DNA (genomic) 6 CGGTATCCTT TTTCCGTACG TTC 23 25 basepairs nucleic acid single linear DNA (genomic) 7 GTTGAAGAGG TGAAGAAAGTTCTCC 25 23 base pairs nucleic acid single linear DNA (genomic) 8GTTCGTCGAT TTCCACGCTT GGC 23 22 base pairs nucleic acid single linearDNA (genomic) 9 AGGGCCTCGT GATACGCCTA TT 22 23 base pairs nucleic acidsingle linear DNA (genomic) 10 ACGAAAACTC ACGTTAAGGG ATT 23

What is claimed is:
 1. A method of shuffling polynucleotides, the methodcomprising: (i) providing a plurality of polynucleotide variants to beshuffled; (ii) conducting a multi-cyclic polynucleotide extensionprocess on at least partially annealed polynucleotide strands havingsequences from the plurality of polynucleotide variants, thepolynucleotide strands having regions of similarity and regions ofheterology with each other, and being at least partially annealedthrough the regions of similarity under conditions whereby one strandserves as a template for extension of another strand with which it ispartially annealed, to generate a population of recombinantpolynucleotides; and, (iii) selecting or screening a recombinantpolynucleotide from the population of recombinant polynucleotides for adesired property, thereby producing an optimized recombinantpolynucleotide having the desired property; wherein the desired propertycomprises: an elevated expression of the recombinant polynucleotide in afirst cell relative to an expression level of one or more of theplurality of polynucleotide variants to be shuffled in the first cell.2. The method of claim 1, wherein the selected optimized recombinantnucleic acid is further recombined with one or more additional nucleicacid to produce at least one further recombined nucleic acid, whereinthe at least one further recombined nucleic acid is selected for thedesired property, thereby producing a further optimized nucleic acid. 3.The method of claim 1, wherein the population of recombinantpolynucleotides is cloned into at least one expression vector, therebyproducing a library of expressed recombinant polynucleotides.
 4. Themethod of claim 3, wherein the library of expressed recombinantpolynucleotides is expressed in a population of cells, thereby producinga library of expressed recombinant polynucleotide cellular expressionproducts.
 5. The method of claim 4, wherein the library of expressedrecombinant polynucleotide cellular expression products comprises alibrary of expressed peptides.
 6. The method of claim 4, wherein thepopulation of cells is screened for the desired property.
 7. The methodof claim 1, wherein at least one cycle of polynucleotide extension isperformed in vitro.
 8. The method of claim 1, the multi-cyclicpolynucleotide extension process comprising: cleaving the plurality ofpolynucleotide variants into fragments; mixing and denaturing thefragments; and, incubating the resulting denatured fragments with apolymerase under conditions which result in annealing of the denaturedfragments and formation of the population of recombinantpolynucleotides.
 9. The method of claim 1, wherein at least a portion ofthe multi-cyclic polynucleotide extension process is performed in a hostcell.
 10. The method of claim 9, wherein the population of recombinantpolynucleotides are expressed in a population of host cells.
 11. Themethod of claim 10, further comprising selecting the population of hostcells for the desired property.
 12. The method of claim 1, wherein thedesired property further comprises an ability encoded by the recombinantpolynucleotide to detect compound A, the method comprising: recombiningat least first and second DNA segments from at least one gene conferringan ability to detect a structurally related compound B, the segmentsdiffering from each other in at least two nucleotides, to produce thepopulation of recombinant polynucleotides; selecting or screening atleast one recombinant gene from the population of recombinantpolynucleotides that confers an optimized ability to detect compound Arelative to a wildtype form of the gene; recombining at least a segmentfrom the at least one recombinant gene with a further DNA segment fromthe at least one gene, the same or different from the first and secondsegments, to produce a further population of recombinant genes;selecting or screening at least one further recombinant gene from thefurther population of recombinant genes that confers optimized abilityto detect compound A relative to a previous recombinant gene; and,repeating the steps as desired, until the further recombinant geneconfers a desired level of optimized ability to detect compound A. 13.The method of claim 12, wherein compound A and compound B are different.14. The method of claim 12, wherein compound A and compound B are thesame.
 15. The method of claim 12, wherein compound A and compound B areindependently selected from: atrazine, benzene, biphenyl, xylene,toluene, camphor, naphtalene, halogenated hydrocarbons, polychlorinatedbiphenyls, polycyclic aromatic hydrocarbons, trichlorethylene,pesticides, and herbicides.
 16. The method of claim 1, wherein thedesired property further comprises an ability encoded by the recombinantpolynucleotide to catalyze a reaction in a cell, wherein the pluralityof polynucleotide variants to be shuffled encodes one or more nucleicacid encoding a dioxygenase.
 17. The method of claim 16, wherein thedioxygenase is from a Pseudomoas species.
 18. The method of claim 1,wherein the desired property further comprises an ability encoded by therecombinant polynucleotide confer enhanced resistance to a heavy metalwhen the recombinant polynucleotide is expressed in a cell, wherein theheavy metal is selected from mercury, arsenate, chromate, cadmium, andsilver.
 19. The method of claim 1, wherein the desired property furthercomprises an ability encoded by the recombinant nucleic acid to producea desired metabolite, the method further comprising detecting thedesired metabolite by mass spectroscopy.
 20. The method of claim 1,wherein the desired property further comprises an ability encoded by therecombinant polynucleotide to utilize a substrate as a nutrient source,wherein the nutrient source is selected from lactose, whey, galactose,mannitol, xylan, cellobiose, cellulose, and sucrose.
 21. The method ofclaim 1, wherein the desired property further comprises an ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo, and wherein: the antibioticis selected from: a peptide, a peptidolactone, a thiopeptide, abeta-lactam, a glycopeptide, a lantibiotic, a microcin, apolyketide-derived antibiotic an anthracyclin, a tetracyclin, amacrolide, an avermectin, a polyether, an ansamycin, a chloramphenicol,an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, acyclosporin, a pepstatin, an actinomycin, a gramicidin, a depsipeptide,a vancomycin and an isoprenoid; the carotenoid is selected from:myxobacton, spheroidene, spheroidenone, lutein, astaxanthin,violaxanthin, 4-ketorulene, myxoxanthrophyll, echinenone, lycopene,zeaxanthin and its mono- and di- glucosides, alpha-, beta-, gamma- anddelta-carotene, beta-cryptoxanthin monoglucoside and neoxanthin; and,the amino acid is selected from phenylalanine, monosodium glutamate,glycine, lysine, threonine, tryptophan, and methionine.
 22. The methodof claim 1, wherein the desired property further comprises an ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo, and wherein the pluralityof polynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding an isoprenoid synthesis gene, agene encoding a trichodiene synthase from Fusarium sprorotrichioides, agene encoding a pentalene synthase from Streptomyces, a gene encoding anaristolochene synthase from Penicillium roquefortii, and a gene encodingan epi-aristolochene synthase from N. tabacum.
 23. The method of claim1, wherein the desired property further comprises an ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo, and wherein the pluralityof polynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding a penicillin N expandase, a geneencoding a penicillin transacylase, a gene encoding a penicillinamidase, a gene encoding a Penicillin G acylase, and a gene encoding aPolyketide synthase.
 24. The method of claim 1, wherein the plurality ofpolynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more gene from: Alcaligenes, Zoogloea, Rhizobium, Bacillus,or an Azobacter which produces a polyhydroxyalkanoates (PHAs), or apolyhyroxybutyrate (PHB).
 25. The method of claim 1, wherein theplurality of polynucleotide variants comprises a nucleic acidsubsequence derived from phbB or phbC.
 26. The method of claim 1,wherein the plurality of polynucleotide variants comprises at least onesubsequence derived from a gene in a cellulose biosynthesis pathway. 27.The method of claim 1, wherein the plurality of polynucleotide variantscomprises at least one subsequence derived from a gene in an E. coliindigo synthesis pathway which synthesizes indigo from glucose via atryptophan/indole pathway.
 28. The method of claim 1, wherein thepartially annealed polynucleotide strands are produced by providingoverlapping single-stranded segments of the polynucleotide variants andincubating under annealing conditions whereby the single-strandedsegments from different polynucleotide variants anneal to form thepartially annealed polynucleotide strands.
 29. The method of claim 28,wherein the overlapping single-stranded segments are random segments ofthe polynucleotide variants.
 30. The method of claim 28, wherein theoverlapping single-stranded segments are non-random segments of thepolynucleotide variants.
 31. The method of claim 28, wherein theplurality of overlapping single-stranded segments are produced bycleaving the population of polynucleotide variants to produce apopulation of overlapping double-stranded fragments and denaturing thedouble-stranded fragments to produce the overlapping single-strandedsegments.
 32. The method of claim 31, wherein the population ofpolynucleotide variants comprise one or more DNA and the cleavage isperformed by DNase I digestion.
 33. The method of claim 1, furthercomprising amplifying the plurality of polynucleotide variants.
 34. Themethod of claim 1, further comprising performing error-prone PCR on atleast one of the polynucleotide variants.
 35. The method of claim 1,wherein the partially annealed polynucleotide strands are produced witha DNA synthesizer.
 36. The method of claim 1, wherein the plurality ofpolynucleotide variants which are shuffled are naturally occurringvariants of a polynucleotide.
 37. The method of claim 36, wherein thenaturally occurring variants of the polynucleotide encode naturalpolypeptides.
 38. The method of claim 36, wherein the naturallyoccurring variants of the polynucleotide comprise one or more of: anaturally occurring human polynucleotide or subsequence thereof, anaturally occurring mouse polynucleotide or subsequence thereof, anaturally occurring bacterial polynucleotide or subsequence thereof, anaturally occurring plant polynucleotide or subsequence thereof, anaturally occurring fungal polynucleotide or subsequence thereof, anaturally occurring animal polynucleotide or subsequence thereof, and anaturally occurring viral polynucleotide or subsequence thereof.
 39. Themethod of claim 36, wherein the naturally occurring variants of thepolynucleotide comprise allelic or non-allelic naturally occurringvariants of the polynucleotide, wherein the allelic or non-allelicnaturally occurring variants are from a single species.
 40. The methodof claim 36, further comprising shuffling a first recombinantpolynucleotide encoding the desired activity with a naturally occurringpolynucleotide and selecting any resulting secondary recombinant nucleicacids for the desired property.
 41. The method of claim 40, wherein thesecondary recombinant nucleic acids are more closely similar in sequenceto the naturally occurring polynucleotide than to the first recombinantpolynucleotide.
 42. The method of claim 36, further comprisingsupplementing the plurality of natural variants of a polynucleotide withinduced variants of a polynucleotide before the amplification process.43. The method of claim 36, further comprising randomly fragmenting thepopulation of natural variants of a polynucleotide before conducting theamplification process.
 44. The method of claim 1, wherein themulti-cyclic polynucleotide extension process comprises PCRamplification of the annealed polynucleotide strands.
 45. The method ofclaim 1, wherein the desired property further comprises an abilityencoded by the optimized recombinant polynucleotide to degrade at leastone halogenated hydrocarbon, wherein the plurality of chosenpolynucleotide variants to be recombined encodes one or more hydrolyticenzyme.
 46. The method of claim 45, wherein the ability encoded by theoptimized recombinant polynucleotide to degrade at least one halogenatedhydrocarbon occurs in a cell.
 47. The method of claim 1, wherein theplurality of polynucleotide variants comprises at least two homologouspolynucleotides.
 48. The method of claim 1, wherein the plurality ofpolynucleotide variants comprises species variants.
 49. The method ofclaim 1, wherein the partially annealed polynucleotide strands areproduced by providing overlapping single-stranded segments of theplurality of polynucleotide variants and incubating under annealingconditions whereby the single-stranded segments from the plurality ofpolynucleotide variants anneal to form the partially annealedpolynucleotide strands.
 50. The method of claim 49, wherein theoverlapping single-stranded segments comprise random segments of thepolynucleotide variants.
 51. The method of claim 49, wherein theoverlapping single-stranded segments comprise selected segments of thepolynucleotide variants.
 52. The method of claim 49, wherein theoverlapping single-stranded segments are synthesized.
 53. A method ofshuffling polynucleotides, the method comprising: (i) providing aplurality of polynucleotide variants to be shuffled; (ii) conducting amulti-cyclic polynucleotide extension process on at least partiallyannealed polynucleotide strands having sequences from the plurality ofpolynucleotide variants, the polynucleotide strands having regions ofsimilarity and regions of heterology with each other, and being at leastpartially annealed through the regions of similarity under conditionswhereby one strand serves as a template for extension of another strandwith which it is partially annealed, to generate a population ofrecombinant polynucleotides; and, (iii) selecting or screening arecombinant polynucleotide from the population of recombinantpolynucleotides for a desired property, thereby producing an optimizedrecombinant polynucleotide having the desired property; wherein thedesired property comprises one or more of: (a) an ability encoded by therecombinant polynucleotide to utilize a substrate as a nutrient source;(b) an ability encoded by the recombinant polynucleotide to detoxify acomposition; or, (c) an ability encoded by the recombinantpolynucleotide to confer enhanced resistance to a heavy metal when therecombinant polynucleotide is expressed in a cell.
 54. The method ofclaim 53, wherein the selected optimized recombinant nucleic acid isfurther recombined with one or more additional nucleic acid to produceat least one further recombined nucleic acid, wherein the at least onefurther recombined nucleic acid is selected for the desired property,thereby producing a further optimized nucleic acid.
 55. The method ofclaim 53, wherein the population of recombinant polynucleotides iscloned into at least one expression vector, thereby producing a libraryof expressed recombinant polynucleotides.
 56. The method of claim 55,wherein the library of expressed recombinant polynucleotides isexpressed in a population of cells, thereby producing a library ofexpressed recombinant polynucleotide cellular expression products. 57.The method of claim 56, wherein the library of expressed recombinantpolynucleotide cellular expression products comprises a library ofexpressed polypeptides.
 58. The method of claim 56, wherein thepopulation of cells is screened for the desired property.
 59. The methodof claim 53, wherein at least one cycle of polynucleotide extension isperformed in vitro.
 60. The method of claim 53, the multi-cyclicpolynucleotide extension process comprising: cleaving the plurality ofpolynucleotide variants into fragments; mixing and denaturing thefragments; and, incubating the resulting denatured fragments with apolymerase under conditions which result in annealing of the denaturedfragments and formation of the population of recombinantpolynucleotides.
 61. The method of claim 53, wherein at least a portionof the multi-cyclic polynucleotide extension process is performed in ahost cell.
 62. The method of claim 61, wherein the population ofrecombinant polynucleotides are expressed in a population of host cells.63. The method of claim 62, further comprising selecting the populationof host cells for the desired property.
 64. The method of claim 53,wherein the desired property is the ability encoded by the recombinantpolynucleotide conferring enhanced resistance to a heavy metal when therecombinant polynucleotide is expressed in a cell, wherein the heavymetal is selected from mercury, arsenate, chromate, cadmium, and silver.65. The method of claim 53, wherein the desired property is the abilityencoded by the recombinant polynucleotide to utilize a substrate as anutrient source, wherein the nutrient source is selected from lactose,whey, galactose, mannitol, xylan, cellobiose, cellulose, and sucrose.66. The method of claim 53, wherein the partially annealedpolynucleotide strands are produced by providing overlappingsingle-stranded segments of the polynucleotide variants and incubatingunder annealing conditions whereby the single-stranded segments fromdifferent polynucleotide variants anneal to form the partially annealedpolynucleotide strands.
 67. The method of claim 66, wherein theoverlapping single-stranded segments are random segments of thepolynucleotide variants.
 68. The method of claim 66, wherein theoverlapping single-stranded segments are non-random segments of thepolynucleotide variants.
 69. The method of claim 66, wherein theplurality of overlapping single-stranded segments are produced bycleaving the population of polynucleotide variants to produce apopulation of overlapping double-stranded fragments and denaturing thedouble-stranded fragments to produce the overlapping single-strandedsegments.
 70. The method of claim 69, wherein the population ofpolynucleotide variants comprise one or more DNAs and the cleavage isperformed by DNase I digestion.
 71. The method of claim 53, furthercomprising amplifying the plurality of polynucleotide variants.
 72. Themethod of claim 53, further comprising performing error-prone PCR on atleast one of the polynucleotide variants.
 73. The method of claim 53,wherein the partially annealed polynucleotide strands are produced witha DNA synthesizer.
 74. The method of claim 53, wherein the plurality ofpolynucleotide variants which are shuffled are naturally occurringvariants of a polynucleotide.
 75. The method of claim 74, wherein thenaturally occurring variants of the polynucleotide encode naturalpolypeptides.
 76. The method of claim 74, wherein the naturallyoccurring variants of the polynucleotide comprise one or more of: anaturally occurring human polynucleotide or subsequence thereof, anaturally occurring mouse polynucleotide or subsequence thereof, anaturally occurring bacterial polynucleotide or subsequence thereof, anaturally occurring plant polynucleotide or subsequence thereof, anaturally occurring fungal polynucleotide or subsequence thereof, anaturally occurring animal polynucleotide or subsequence thereof, and anaturally occurring viral polynucleotide or subsequence thereof.
 77. Themethod of claim 74, wherein the naturally occurring variants of thepolynucleotide comprise allelic or non-allelic naturally occurringvariants of the polynucleotide, wherein the allelic or non-allelicnaturally occurring variants are from a single species.
 78. The methodof claim 74, further comprising shuffling a first recombinantpolynucleotide encoding the desired activity with a naturally occurringpolynucleotide and selecting any resulting secondary recombinant nucleicacids for the desired property.
 79. The method of claim 78, wherein thesecondary recombinant nucleic acids are more closely similar in sequenceto the naturally occurring polynucleotide than to the first recombinantpolynucleotide.
 80. The method of claim 74, further comprisingsupplementing the plurality of naural variants of a polynucleotide withinduced variants of a polynucleotide before the amplification process.81. The method of claim 74, further comprising randomly fragmenting thepopulation of natural variants of a polynucleotide before conducting theamplification process.
 82. The method of claim 53, wherein themulti-cyclic polynucleotide extension process comprises PCRamplification of the annealed polynucleotide strands.
 83. The method ofclaim 53, wherein the desired property is an ability encoded by theoptimized recombinant polynucleotide to degrade at least one halogenatedhydrocarbon, wherein the plurality of chosen polynucleotide variants tobe recombined encodes one or more hydrolytic enzyme.
 84. The method ofclaim 83, wherein the ability encoded by the optimized recombinantpolynucleotide to degrade at least one halogenated hydrocarbon occurs ina cell.
 85. A method of shuffling polynucleotides, the methodcomprising: (i) providing a plurality of polynucleotide variants to beshuffled; (ii) conducting a multi-cyclic polynucleotide extensionprocess on at least partially annealed polynucleotide strands havingsequences from the plurality of polynucleotide variants, thepolynucleotide strands having regions of similarity and regions ofheterology with each other, and being at least partially annealedthrough the regions of similarity under conditions whereby one strandserves as a template for extension of another strand with which it ispartially annealed, to generate a population of recombinantpolynucleotides; and, (iii) selecting or screening a recombinantpolynucleotide from the population of recombinant polynucleotides for adesired property, thereby producing an optimized recombinantpolynucleotide having the desired property; wherein the desired propertycomprises: an ability encoded by the recombinant polynucleotide tocatalyze a reaction of interest, wherein the reaction of interest is notsubstantially catalyzed by the plurality of polynucleotide variants tobe shuffled.
 86. The method of claim 85, wherein the selected optimizedrecombinant nucleic acid is further recombined with one or moreadditional nucleic acid to produce at least one further recombinednucleic acid, wherein the at least one further recombined nucleic acidis selected for the desired property, thereby producing a furtheroptimized nucleic acid.
 87. The method of claim 85, wherein thepopulation of recombinant polynucleotides is cloned into at least oneexpression vector, thereby producing a library of expressed recombinantpolynucleotides.
 88. The method of claim 87, wherein the library ofexpressed recombinant polynucleotides is expressed in a population ofcells, thereby producing a library of expressed recombinantpolynucleotide cellular expression products.
 89. The method of claim 88,wherein the library of expressed recombinant polynucleotide cellularexpression products comprises a library of expressed polypeptides. 90.The method of claim 88, wherein the population of cells is screened forthe desired property.
 91. The method of claim 85, wherein at least onecycle of polynucleotide extension is performed in vitro.
 92. The methodof claim 85, the multi-cyclic polynucleotide extension processcomprising: cleaving the plurality of polynucleotide variants intofragments; mixing and denaturing the fragments; and, incubating theresulting denatured fragments with a polymerase under conditions whichresult in annealing of the denatured fragments and formation of thepopulation of recombinant polynucleotides.
 93. The method of claim 85,wherein at least a portion of the multi-cyclic polynucleotide extensionprocess is performed in a host cell.
 94. The method of claim 93, whereinthe population of recombinant polynucleotides are expressed in apopulation of host cells.
 95. The method of claim 94, further comprisingselecting the population of host cells for the desired property.
 96. Themethod of claim 85, wherein the plurality of polynucleotide variants tobe shuffled encodes one or more nucleic acid encoding a dioxygenase. 97.The method of claim 96, wherein the dioxygenase is from a Pseudomonasspecies.
 98. The method of claim 85, wherein the reaction of interestcomprises an ability encoded by the recombinant polynucleotide to detectcompound A, the method comprising: recombining at least first and secondDNA segments from at least one gene conferring an ability to detect astructurally related compound B, the segments differing from each otherin at least two nucleotides, to produce the population of recombinantpolynucleotides; selecting or screening at least one recombinant genefrom the population of recombinant polynucleotides that confers anoptimized ability to detect compound A relative to a wildtype form ofthe gene; recombining at least a segment from the at least onerecombinant gene with a further DNA segment from the at least one gene,the same or different from the first and second segments, to produce afurther population of recombinant genes; selecting or screening at leastone further recombinant gene from the further population of recombinantgenes that confers optimized ability to detect compound A relative to aprevious recombinant gene; and, repeating the steps as desired, untilthe further recombinant gene confers a desired level of optimizedability to detect compound A.
 99. The method of claim 98, whereincompound A and compound B are different.
 100. The method of claim 98,wherein compound A and compound B are the same.
 101. The method of claim98, wherein compound A and compound B are independently selected from:atrazine, benzene, biphenyl, xylene, toluene, camphor, naphtalene,halogenated hydrocarbons, polychlorinated biphenyls, polycyclic aromatichydrocarbons, trichlorethylene, pesticides, and herbicides.
 102. Themethod of claim 85, wherein the the plurality of polynucleotide variantsto be shuffled encodes one or more nucleic acid encoding a dioxygenase.103. The method of claim 102, wherein the dioxygenase is from aPseudomonas species.
 104. The method of claim 85, wherein the reactionof interest confers enhanced resistance to a heavy metal when therecombinant polynucleotide is expressed in a cell, wherein the heavymetal is selected from mercury, arsenate, chromate, cadmium, and silver.105. The method of claim 85, wherein the reaction of interest produces adesired metabolite, the method further comprising detecting the desiredmetabolite by mass spectroscopy.
 106. The method of claim 85, whereinthe reaction of interest provides utilization of a substrate as anutrient source, wherein the nutrient source is selected from lactose,whey, galactose, mannitol, xylan, cellobiose, cellulose, and sucrose.107. The method of claim 85, wherein the reaction of interest comprisesynthesis of an isoprenoid, a polyketide, a carotenoid, an antibiotic,an amino acid, a polymer, vitamin C, or indigo, and wherein: theantibiotic is selected from: a peptide, a peptidolactone, a thiopeptide,a beta-lactam, a glycopeptide, a lantibiotic, a microcin, apolyketide-derived antibiotic an anthracyclin, a tetracyclin, amacrolide, an avermectin, a polyether, an ansamycin, a chloramphenicol,an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, acyclosporin, a pepstatin, an actinomycin, a gramicidin, a depsipeptide,a vancomycin and an isoprenoid; the carotenoid is selected from:myxobacton, spheroidene, spheroidenone, lutein, astaxanthin,violaxanthin, 4-ketorulene, myxoxanthrophyll, echinenone, lycopene,zeaxanthin and its mono- and di- glucosides, alpha-, beta-, gamma- anddelta-carotene, beta-cryptoxanthin monoglucoside and neoxanthin; and,the amino acid is selected from phenylalanine, monosodium glutamate,glycine, lysine, threonine, tryptophan, and methionine.
 108. The methodof claim 85, wherein the reaction of interest comprises synthesis of anisoprenoid, a polyketide, a carotenoid, an antibiotic, an amino acid, apolymer, vitamin C, or indigo, and wherein the plurality ofpolynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding an isoprenoid synthesis gene, agene encoding a trichodiene synthase from Fusarium sprorotrichioides, agene encoding a pentalene synthase from Streptomyces, a gene encoding anaristolochene synthase from Penicillium roquefortii, and a gene encodingan epi-aristolochene synthase from N. tabacum.
 109. The method of claim85, wherein the reaction of interest comprises synthesis of anisoprenoid, a polyketide, a carotenoid, an antibiotic, an amino acid, apolymer, vitamin C, or indigo, and wherein the plurality ofpolynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding a penicillin N expandase, a geneencoding a penicillin transacylase, a gene encoding a penicillinamidase, a gene encoding a Penicillin G acylase, and a gene encoding aPolyketide synthase.
 110. The method of claim 85, wherein the pluralityof polynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more gene from: Alcaligenes, Zoogloea, Rhizobium, Bacillus,or an Azobacter which produces a polyhydroxyalkanoates (PHAs), or apolyhyroxybutyrate (PHB).
 111. The method of claim 85, wherein theplurality of polynucleotide variants comprises a nucleic acidsubsequence derived from phbB or phbC.
 112. The method of claim 85,wherein the plurality of polynucleotide variants comprises at least onesubsequence derived from a gene in a cellulose biosynthesis pathway.113. The method of claim 85, wherein the plurality of polynucleotidevariants comprises at least one subsequence derived from a gene in an E.coli indigo synthesis pathway which synthesizes indigo from glucose viaa tryptophan/indole pathway.
 114. The method of claim 85, wherein thepartially annealed polynucleotide strands are produced by providingoverlapping single-stranded segments of the polynucleotide variants andincubating under annealing conditions whereby the single-strandedsegments from different polynucleotide variants anneal to form thepartially annealed polynucleotide strands.
 115. The method of claim 114,wherein the overlapping single-stranded segments are random segments ofthe polynucleotide variants.
 116. The method of claim 114, wherein theoverlapping single-stranded segments are non-random segments of thepolynucleotide variants.
 117. The method of claim 114, wherein theplurality of overlapping single-stranded segments are produced bycleaving the population of polynucleotide variants to produce apopulation of overlapping double-stranded fragments and denaturing thedouble-stranded fragments to produce the overlapping single-strandedsegments.
 118. The method of claim 117, wherein the population ofpolynucleotide variants comprise one or more DNAs and the cleavage isperformed by DNase I digestion.
 119. The method of claim 85, furthercomprising amplifying the plurality of polynucleotide variants.
 120. Themethod of claim 85, further comprising performing error-prone PCR on atleast one of the polynucleotide variants.
 121. The method of claim 85,wherein the partially annealed polynucleotide strands are produced witha DNA synthesizer.
 122. The method of claim 85, wherein the plurality ofpolynucleotide variants which are shuffled are naturally occurringvariants of a polynucleotide.
 123. The method of claim 122, wherein thenaturally occurring variants of the polynucleotide encode naturalpolypeptides.
 124. The method of claim 122, wherein the naturallyoccurring variants of the polynucleotide comprise one or more of: anaturally occurring human polynucleotide or subsequence thereof, anaturally occurring mouse polynucleotide or subsequence thereof, anaturally occurring bacterial polynucleotide or subsequence thereof, anaturally occurring plant polynucleotide or subsequence thereof, anaturally occurring fungal polynucleotide or subsequence thereof, anaturally occurring animal polynucleotide or subsequence thereof, and anaturally occurring viral polynucleotide or subsequence thereof. 125.The method of claim 122, wherein the naturally occurring variants of thepolynucleotide comprise allelic or non-allelic naturally occurringvariants of the polynucleotide, wherein the allelic or non-allelicnaturally occurring variants are from a single species.
 126. The methodof claim 122, further comprising shuffling a first recombinantpolynucleotide encoding the desired activity with a naturally occurringpolynucleotide and selecting any resulting secondary recombinant nucleicacids for the desired property.
 127. The method of claim 126, whereinthe secondary recombinant nucleic acids are more closely similar insequence to the naturally occurring polynucleotide than to the firstrecombinant polynucleotide.
 128. The method of claim 122, furthercomprising supplementing the plurality of naural variants of apolynucleotide with induced variants of a polynucleotide before theamplification process.
 129. The method of claim 122, further comprisingrandomly fragmenting the population of natural variants of apolynucleotide before conducting the amplification process.
 130. Themethod of claim 85, wherein the multi-cyclic polynucleotide extensionprocess comprises PCR amplification of the annealed polynucleotidestrands.
 131. The method of claim 85, wherein the reaction of interestdegrades at least one halogenated hydrocarbon, wherein the plurality ofchosen polynucleotide variants to be recombined encodes one or morehydrolytic enzyme.
 132. The method of claim 131, wherein the abilityencoded by the optimized recombinant polynucleotide to degrade at leastone halogenated hydrocarbon occurs in a cell.
 133. The method of claim85, wherein the plurality of polynucleotide variants comprises at leasttwo homologous polynucleotides.
 134. The method of claim 85, wherein theplurality of polynucleotide variants comprises species variants. 135.The method of claim 85, wherein the partially annealed polynucleotidestrands are produced by providing overlapping single-stranded segmentsof the plurality of polynucleotide variants and incubating underannealing conditions whereby the single-stranded segments from theplurality of polynucleotide variants anneal to form the partiallyannealed polynucleotide strands.
 136. The method of claim 135, whereinthe overlapping single-stranded segments comprise random segments of thepolynucleotide variants.
 137. The method of claim 135, wherein theoverlapping single-stranded segments comprise selected segments of thepolynucleotide variants.
 138. The method of claim 135, wherein theoverlapping single-stranded segments are synthesized.
 139. A method ofshuffling polynucleotides, the method comprising: (i) providing aplurality of polynucleotide variants to be shuffled; (ii) conducting amulti-cyclic polynucleotide extension process on at least partiallyannealed polynucleotide strands having sequences from the plurality ofpolynucleotide variants, the polynucleotide strands having regions ofsimilarity and regions of heterology with each other, and being at leastpartially annealed through the regions of similarity under conditionswhereby one strand serves as a template for extension of another strandwith which it is partially annealed, to generate a population ofrecombinant polynucleotides; and, (iii) selecting or screening arecombinant polynucleotide from the population of recombinantpolynucleotides for a desired property, thereby producing an optimizedrecombinant polynucleotide having the desired property; wherein thedesired property comprises one or more of: (a) an ability encoded by therecombinant polynucleotide to catalyze a reaction in a cell, or, (b) anability encoded by the recombinant polynucleotide to detect a compound.140. The method of claim 139, wherein the selected optimized recombinantnucleic acid is further recombined with one or more additional nucleicacid to produce at least one further recombined nucleic acid, whereinthe at least one further recombined nucleic acid is selected for thedesired property, thereby producing a further optimized nucleic acid.141. The method of claim 139, wherein the population of recombinantpolynucleotides is cloned into at least one expression vector, therebyproducing a library of expressed recombinant polynucleotides.
 142. Themethod of claim 141, wherein the library of expressed recombinantpolynucleotides is expressed in a population of cells, thereby producinga library of expressed recombinant polynucleotide cellular expressionproducts.
 143. The method of claim 142, wherein the library of expressedrecombinant polynucleotide cellular expression products comprises alibrary of expressed polypeptides.
 144. The method of claim 142, whereinthe population of cells is screened for the desired property.
 145. Themethod of claim 139, wherein at least one cycle of polynucleotideextension is performed in vitro.
 146. The method of claim 139, themulti-cyclic polynucleotide extension process comprising: cleaving theplurality of polynucleotide variants into fragments; mixing anddenaturing the fragments; and, incubating the resulting denaturedfragments with a polymerase under conditions which result in annealingof the denatured fragments and formation of the population ofrecombinant polynucleotides.
 147. The method of claim 139, wherein atleast a portion of the multi-cyclic polynucleotide extension process isperformed in a host cell.
 148. The method of claim 147, wherein thepopulation of recombinant polynucleotides are expressed in a populationof host cells.
 149. The method of claim 148, further comprisingselecting the population of host cells for the desired property. 150.The method of claim 139, wherein the desired property is an abilityencoded by the recombinant polynucleotide to detect compound A, themethod comprising: recombining at least first and second DNA segmentsfrom at least one gene conferring an ability to detect a structurallyrelated compound B, the segments differing from each other in at leasttwo nucleotides, to produce the population of recombinantpolynucleotides; selecting or screening at least one recombinant genefrom the population of recombinant polynucleotides that confers anoptimized ability to detect compound A relative to a wildtype form ofthe gene; recombining at least a segment from the at least onerecombinant gene with a further DNA segment from the at least one gene,the same or different from the first and second segments, to produce afurther population of recombinant genes; selecting or screening at leastone further recombinant gene from the further population of recombinantgenes that confers optimized ability to detect compound A relative to aprevious recombinant gene; and, repeating the steps as desired, untilthe further recombinant gene confers a desired level of optimizedability to detect compound A.
 151. The method of claim 150, whereincompound A and compound B are different.
 152. The method of claim 150,wherein compound A and compound B are the same.
 153. The method of claim150, wherein compound A and compound B are independently selected from:atrazine, benzene, biphenyl, xylene, toluene, camphor, napthalene,halogenated hydrocarbons, polychlorinated biphenyls, polycyclic aromatichydrocarbons, trichlorethylene, pesticides, and herbicides.
 154. Themethod of claim 139, wherein the desired property is the ability encodedby the recombinant polynucleotide to catalyze a reaction in a cell,wherein the plurality of polynucleotide variants to be shuffled encodesone or more nucleic acid encoding a dioxygenase.
 155. The method ofclaim 154, wherein the dioxygenase is from a Pseudomonas species. 156.The method of claim 139, wherein the reaction in the cell confersenhanced resistance of the cell to a heavy metal when the recombinantpolynucleotide is expressed in the cell, wherein the heavy metal isselected from mercury, arsenate, chromate, cadmium, and silver.
 157. Themethod of claim 139, wherein the reaction in the cell provides forproduction of a desired metabolite in the cell.
 158. The method of claim157, the method further comprising detecting the desired metabolite bymass spectroscopy.
 159. The method of claim 139, wherein the reactionprovides the cell with an ability to utilize a substrate as a nutrientsource, wherein the nutrient source is selected from lactose, whey,galactose, mannitol, xylan, cellobiose, cellulose, and sucrose.
 160. Themethod of claim 139, wherein the reaction provides the cell with anability to synthesize an isoprenoid, a polyketide, a carotenoid, anantibiotic, an amino acid, a polymer, vitamin C, or indigo.
 161. Themethod of claim 139, wherein the reaction provides the cell with anability to synthesize an isoprenoid, a polyketide, a carotenoid, anantibiotic, an amino acid, a polymer, vitamin C, or indigo and wherein:the antibiotic is selected from: a peptide, a peptidolactone, athiopeptide, a beta-lactam, a glycopeptide, a lantibiotic, a microcin, apolyketide-derived antibiotic an anthracyclin, a tetracyclin, amacrolide, an avermectin, a polyether, an ansamycin, a chloramphenicol,an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, acyclosporin, a pepstatin, an actinomycin, a gramicidin, a depsipeptide,a vancomycin and an isoprenoid; the carotenoid is selected from:myxobacton, spheroidene, spheroidenone, lutein, astaxanthin,violaxanthin, 4-ketorulene, myxoxanthrophyll, echinenone, lycopene,zeaxanthin and its mono- and di- glucosides, alpha-, beta-, gamma- anddelta-carotene, beta-cryptoxanthin monoglucoside and neoxanthin; and,the amino acid is selected from phenylalanine, monosodium glutamate,glycine, lysine, threonine, tryptophan, and methionine.
 162. The methodof claim 139, wherein the reaction provides the cell with an ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo and, and wherein theplurality of polynucleotide variants comprises a nucleic acidsubsequence derived from one or more of: a gene encoding an isoprenoidsynthesis gene, a gene encoding a trichodiene synthase from Fusariumsprorotrichioides, a gene encoding a pentalene synthase fromStreptomyces, a gene encoding an aristolochene synthase from Penicilliumroquefortii, and a gene encoding an epi-aristolochene synthase from N.tabacum.
 163. The method of claim 139, wherein the reaction provides thecell with an ability to synthesize an isoprenoid, a polyketide, acarotenoid, an antibiotic, an amino acid, a polymer, vitamin C, orindigo, and wherein the plurality of polynucleotide variants comprises anucleic acid subsequence derived from one or more of: a gene encoding apenicillin N expandase, a gene encoding a penicillin transacylase, agene encoding a penicillin amidase, a gene encoding a Penicillin Gacylase, and a gene encoding a Polyketide synthase.
 164. The method ofclaim 139, wherein the plurality of polynucleotide variants comprises anucleic acid subsequence derived from one or more gene from:Alcaligenes, Zoogloea, Rhizobium, Bacillus, or an Azobacter whichproduces a polyhydroxyalkanoates (PHAs), or a polyhyroxybutyrate (PHB).165. The method of claim 139, wherein the plurality of polynucleotidevariants comprises a nucleic acid subsequence derived from phbB or phbC.166. The method of claim 139, wherein the plurality of polynucleotidevariants comprises at least one subsequence derived from a gene in acellulose biosynthesis pathway.
 167. The method of claim 139, whereinthe plurality of polynucleotide variants comprises at least onesubsequence derived from a gene in an E. coli indigo synthesis pathwaywhich synthesizes indigo from glucose via a tryptophan/indole pathway.168. The method of claim 139, wherein the partially annealedpolynucleotide strands are produced by providing overlappingsingle-stranded segments of the polynucleotide variants and incubatingunder annealing conditions whereby the single-stranded segments fromdifferent polynucleotide variants anneal to form the partially annealedpolynucleotide strands.
 169. The method of claim 168, wherein theoverlapping single-stranded segments are random segments of thepolynucleotide variants.
 170. The method of claim 168, wherein theoverlapping single-stranded segments are non-random segments of thepolynucleotide variants.
 171. The method of claim 168, wherein theplurality of overlapping single-stranded segments are produced bycleaving the population of polynucleotide variants to produce apopulation of overlapping double-stranded fragments and denaturing thedouble-stranded fragments to produce the overlapping single-strandedsegments.
 172. The method of claim 31, wherein the population ofpolynucleotide variants comprise one or more DNAs and the cleavage isperformed by DNase I digestion.
 173. The method of claim 139, furthercomprising amplifying the plurality of polynucleotide variants.
 174. Themethod of claim 139, further comprising performing error-prone PCR on atleast one of the polynucleotide variants.
 175. The method of claim 139,wherein the partially annealed polynucleotide strands are produced witha DNA synthesizer.
 176. The method of claim 139, wherein the pluralityof polynucleotide variants which are shuffled are naturally occurringvariants of a polynucleotide.
 177. The method of claim 176, wherein thenaturally occurring variants of the polynucleotide encode naturalpolypeptides.
 178. The method of claim 177, wherein the naturallyoccurring variants of the polynucleotide comprise one or more of: anaturally occurring human polynucleotide or subsequence thereof, anaturally occurring mouse polynucleotide or subsequence thereof, anaturally occurring bacterial polynucleotide or subsequence thereof, anaturally occurring plant polynucleotide or subsequence thereof, anaturally occurring fungal polynucleotide or subsequence thereof, anaturally occurring animal polynucleotide or subsequence thereof, and anaturally occurring viral polynucleotide or subsequence thereof. 179.The method of claim 177, wherein the naturally occurring variants of thepolynucleotide comprise allelic or non-allelic naturally occurringvariants of the polynucleotide, wherein the allelic or non-allelicnaturally occurring variants are from a single species.
 180. The methodof claim 177, further comprising shuffling a first recombinantpolynucleotide encoding the desired activity with a naturally occurringpolynucleotide and selecting any resulting secondary recombinant nucleicacids for the desired property.
 181. The method of claim 180, whereinthe secondary recombinant nucleic acids are more closely similar insequence to the naturally occurring polynucleotide than to the firstrecombinant polynucleotide.
 182. The method of claim 177, furthercomprising supplementing the plurality of naural variants of apolynucleotide with induced variants of a polynucleotide before theamplification process.
 183. The method of claim 177, further comprisingrandomly fragmenting the population of natural variants of apolynucleotide before conducting the amplification process.
 184. Themethod of claim 139, wherein the multi-cyclic polynucleotide extensionprocess comprises PCR amplification of the annealed polynucleotidestrands.
 185. The method of claim 139, wherein the reaction confers anability to degrade at least one halogenated hydrocarbon to the cell,wherein the plurality of chosen polynucleotide variants to be recombinedencodes one or more hydrolytic enzyme.
 186. The method of claim 185,wherein the ability encoded by the optimized recombinant polynucleotideto degrade at least one halogenated hydrocarbon occurs in a cell.
 187. Amethod of shuffling polynucleotides, the method comprising: (i)providing a plurality of polynucleotide variants to be shuffled; (ii)conducting a multi-cyclic polynucleotide extension process on at leastpartially annealed polynucleotide strands having sequences from theplurality of polynucleotide variants, the polynucleotide strands havingregions of similarity and regions of heterology with each other, andbeing at least partially annealed through the regions of similarityunder conditions whereby one strand serves as a template for extensionof another strand with which it is partially annealed, to generate apopulation of recombinant polynucleotides; and, (iii) selecting orscreening a recombinant polynucleotide from the population ofrecombinant polynucleotides for a desired property, thereby producing anoptimized recombinant polynucleotide having the desired property;wherein the desired property comprises one or more property selectedfrom the group consisting of: (a) an ability encoded by the recombinantnucleic acid to produce a desired metabolite; and, (b) an ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo.
 188. The method of claim187, wherein the selected optimized recombinant nucleic acid is furtherrecombined with one or more additional nucleic acid to produce at leastone further recombined nucleic acid, wherein the at least one furtherrecombined nucleic acid is selected for the desired property, therebyproducing a further optimized nucleic acid.
 189. The method of claim187, wherein the population of recombinant polynucleotides is clonedinto at least one expression vector, thereby producing a library ofexpressed recombinant polynucleotides.
 190. The method of claim 189,wherein the library of expressed recombinant polynucleotides isexpressed in a population of cells, thereby producing a library ofexpressed recombinant polynucleotide cellular expression products. 191.The method of claim 190, wherein the library of expressed recombinantpolynucleotide cellular expression products comprises a library ofexpressed polypeptides.
 192. The method of claim 190, wherein thepopulation of cells is screened for the desired property.
 193. Themethod of claim 187, wherein at least one cycle of polynucleotideextension is performed in vitro.
 194. The method of claim 187, themulti-cyclic polynucleotide extension process comprising: cleaving theplurality of polynucleotide variants into fragments; mixing anddenaturing the fragments; and, incubating the resulting denaturedfragments with a polymerase under conditions which result in annealingof the denatured fragments and formation of the population ofrecombinant polynucleotides.
 195. The method of claim 187, wherein atleast a portion of the multi-cyclic polynucleotide extension process isperformed in a host cell.
 196. The method of claim 195, wherein thepopulation of recombinant polynucleotides are expressed in a populationof host cells.
 197. The method of claim 196, further comprisingselecting the population of host cells for the desired property. 198.The method of claim 187, wherein the desired property is the ability tosynthesize an isoprenoid, a polyketide, a carotenoid, an antibiotic, anamino acid, a polymer, vitamin C, or indigo, and wherein: the antibioticis selected from: a peptide, a peptidolactone, a thiopeptide, abeta-lactam, a glycopeptide, a lantibiotic, a microcin, apolyketide-derived antibiotic an anthracyclin, a tetracyclin, amacrolide, an avermectin, a polyether, an ansamycin, a chloramphenicol,an aminoglycoside, an aminocyclitol, a polyoxin, an agrocin, acyclosporin, a pepstatin, an actinomycin, a gramicidin, a depsipeptide,a vancomycin and an isoprenoid; the carotenoid is selected from:myxobacton, spheroidene, spheroidenone, lutein, astaxanthin,violaxanthin, 4-ketorulene, myxoxanthrophyll, echinenone, lycopene,zeaxanthin and its mono- and di- glucosides, alpha-, beta-, gamma- anddelta-carotene, beta-cryptoxanthin monoglucoside and neoxanthin; and,the amino acid is selected from phenylalanine, monosodium glutamate,glycine, lysine, threonine, tryptophan, and methionine.
 199. The methodof claim 187, wherein the desired property is the ability to synthesizean isoprenoid, a polyketide, a carotenoid, an antibiotic, an amino acid,a polymer, vitamin C, or indigo, and wherein the plurality ofpolynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding an isoprenoid synthesis gene, agene encoding a trichodiene synthase from Fusarium sprorotrichioides, agene encoding a pentalene synthase from Streptomyces, a gene encoding anaristolochene synthase from Penicillium roquefortii, and a gene encodingan epi-aristolochene synthase from N. tabacum.
 200. The method of claim187, wherein the desired property is the ability to synthesize anisoprenoid, a polyketide, a carotenoid, an antibiotic, an amino acid, apolymer, vitamin C, or indigo, and wherein the plurality ofpolynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more of: a gene encoding a penicillin N expandase, a geneencoding a penicillin transacylase, a gene encoding a penicillinamidase, a gene encoding a Penicillin G acylase, and a gene encoding aPolyketide synthase.
 201. The method of claim 187, wherein the pluralityof polynucleotide variants comprises a nucleic acid subsequence derivedfrom one or more gene from: Alcaligenes, Zoogloea, Rhizobium, Bacillus,or an Azobacter which produces a polyhydroxyalkanoates (PHAs), or apolyhydroxybutyrate (PHB).
 202. The method of claim 187, wherein theplurality of polynucleotide variants comprises a nucleic acidsubsequence derived from phbB or phbC.
 203. The method of claim 187,wherein the plurality of polynucleotide variants comprises at least onesubsequence derived from a gene in a cellulose biosynthesis pathway.204. The method of claim 187, wherein the plurality of polynucleotidevariants comprises at least one subsequence derived from a gene in an E.coli indigo synthesis pathway which synthesizes indigo from glucose viaa tryptophan/indole pathway.
 205. The method of claim 187, wherein thepartially annealed polynucleotide strands are produced by providingoverlapping single-stranded segments of the polynucleotide variants andincubating under annealing conditions whereby the single-strandedsegments from different polynucleotide variants anneal to form thepartially annealed polynucleotide strands.
 206. The method of claim 205,wherein the overlapping single-stranded segments are random segments ofthe polynucleotide variants.
 207. The method of claim 205, wherein theoverlapping single-stranded segments are non-random segments of thepolynucleotide variants.
 208. The method of claim 205, wherein theplurality of overlapping single-stranded segments are produced bycleaving the population of polynucleotide variants to produce apopulation of overlapping double-stranded fragments and denaturing thedouble-stranded fragments to produce the overlapping single-strandedsegments.
 209. The method of claim 208, wherein the population ofpolynucleotide variants comprise one or more DNAs and the cleavage isperformed by DNase I digestion.
 210. The method of claim 187, furthercomprising amplifying the plurality of polynucleotide variants.
 211. Themethod of claim 187, further comprising performing error-prone PCR on atleast one of the chosen polynucleotide variants.
 212. The method ofclaim 187, wherein the partially annealed polynucleotide strands areproduced with a DNA synthesizer.
 213. The method of claim 187, whereinthe plurality of polynucleotide variants which are shuffled arenaturally occurring variants of a polynucleotide.
 214. The method ofclaim 213, wherein the naturally occurring variants of thepolynucleotide encode natural polypeptides.
 215. The method of claim213, wherein the naturally occurring variants of the polynucleotidecomprise one or more of: a naturally occurring human polynucleotide orsubsequence thereof, a naturally occurring mouse polynucleotide orsubsequence thereof, a naturally occurring bacterial polynucleotide orsubsequence thereof, a naturally occurring plant polynucleotide orsubsequence thereof, a naturally occurring fungal polynucleotide orsubsequence thereof, a naturally occurring animal polynucleotide orsubsequence thereof, and a naturally occurring viral polynucleotide orsubsequence thereof.
 216. The method of claim 214, wherein the naturallyoccurring variants of the polynucleotide comprise allelic or non-allelicnaturally occurring variants of the polynucleotide, wherein the allelicor non-allelic naturally occurring variants are from a single species.217. The method of claim 214, further comprising shuffling a firstrecombinant polynucleotide encoding the desired activity with anaturally occurring polynucleotide and selecting any resulting secondaryrecombinant nucleic acids for the desired property.
 218. The method ofclaim 217, wherein the secondary recombinant nucleic acids are moreclosely similar in sequence to the naturally occurring polynucleotidethan to the first recombinant polynucleotide.
 219. The method of claim214, further comprising supplementing the plurality of naural variantsof a polynucleotide with induced variants of a polynucleotide before theamplification process.
 220. The method of claim 214, further comprisingrandomly fragmenting the population of natural variants of apolynucleotide before conducting the amplification process.
 221. Themethod of claim 187, wherein the multi-cyclic polynucleotide extensionprocess comprises PCR amplification of the annealed polynucleotidestrands.
 222. The method of claim 187, wherein the desired property isan ability encoded by the optimized recombinant polynucleotide todegrade at least one halogenated hydrocarbon, wherein the plurality ofchosen polynucleotide variants to be recombined encodes one or morehydrolytic enzyme.
 223. The method of claim 222, wherein the abilityencoded by the optimized recombinant polynucleotide to degrade at leastone halogenated hydrocarbon occurs in a cell.
 224. A method of providingan optimized recombinant hydrolytic enzyme comprising shuffling two ormore polynucleotides which are derived from one or more hydrolyticenzyme coding polynucleotides.
 225. The method of claim 224, furthercomprising the steps of: conducting a multi-cyclic polynucleotideextension process on at least partially annealed polynucleotide strandscomprising sequences from a plurality of chosen hydrolytic enzyme codingpolynucleotide variants, the polynucleotide strands comprising regionsof similarity and regions of heterology with each other, and being atleast partially annealed through the regions of similarity underconditions whereby one strand serves as a template for extension ofanother strand with which it is partially annealed, to generate apopulation of recombinant hydrolytic enzyme polynucleotides; and,selecting or screening a recombinant hydrolytic enzyme polynucleotidefrom the population of recombinant hydrolytic enzyme polynucleotides foran ability to degrade at least one halogenated hydrocarbon, therebyproviding an optimized recombinant hydrolytic enzyme.